prm". I would be > happy if somebody could point me out to some scripts which help me performDCD. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. 7b1 on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallIn reply to: Gianluca Interlandi: "Compiling NAMD 2. Thanks for the reply. From: Gianluca Interlandi <gianluca_at_u. I > attach a plot of a constant velocity simulation where I'm pulling two > proteins apart. Just source the Tcl file and use the 'unwrap' procedure. Neil King Assistant Professor. From: Gianluca Interlandi (gianluca_at_u. Thomas, 2 , * and Evgeni V. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. The simulations were not performed at constant velocity > but at constant force. edu) Date: Wed Sep 18 2013 - 13:53:55 CDT Next message: Axel Kohlmeyer: "Re: Open VMD from a remote host" Previous message: Gianluca Interlandi: "Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Axel Kohlmeyer:. What can be the possible cause for this or does it happens naturally> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. washington. upenn. 5923 Kcal/mol also we have 6. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping coefficient" Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Proteins 78, 2506–2522 [PMC free article] [Google Scholar] > On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. edu> > wrote: > Roy, > > I think that you are confusing two things. The simulations were not performed at constant velocity > but at constant force. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. 7 released". edu> > wrote:Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. washington. From: Buddhadev Maiti (bmaiti_at_gsu. 7b1 on NCSA Abe. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Interlandi G. The more tasks you have the > more frequently the CPUs need to update each other. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. Next message: Gianluca Interlandi: "Infiniband and PME gridsize" Previous message: nordgren_at_sas. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. From: Gianluca Interlandi (gianluca_at_u. washington. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. washington. edu) Date: Tue Sep 15 2020 - 20:34:44 CDT Next message: Kodituwakku,Dimuthu Nirmani: "Re: Post processing NAMD trajectory" Previous message: Victor Zhao: "Re: Re: AMBER input and REST2 leads to crash" Next in thread:. unizh. 7 out the door on Friday. washington. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you can> 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. /night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum stay: 2 night(s) Book online - Book holiday rental 11131246 with Vrbo. edu> wrote: > Hi Fatemeh, > > Thanks for replying. washington. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. washington. washington. Hope the video helps, but now I'm embarrassed. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in. Comparative controls consisted of FocH (high affinity with and. I was getting 2. 6 version, although I am not running the cluster at full load yet. e. . The Netherlands) is an antibody raised against K12 FimH-lectin domain (residues 1–160) and previously determined to recognize or induce the high affinity state of K12 FimH, especially in the presence of ligand ( buffer in wells of 96-well flat-bottom plates at 37 °C for 1 h. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. Check the NAMD log! Any errors or warnings?"wrapAll on" with a complex. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. washington. washington. washington. washington. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. edu: "Re: high (or low) pressure readings" Next in thread: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Brian Bennion: "Re: fatal error"> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. The server where VMD is started from has On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. >Re: Vibrational mode analysis. uiuc. Name : Current Position : Tim Connolley, Bioengineering 2005 : Michigan State Mechanical Engineering Graduate Program: Brett Anderson, Bioengineering 2006Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthCorrespondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)"Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. washington. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and. Department of Bioengineering, University of Washington, Seattle, Washington, 98195. 97 pN*nm = 1 Kcal/molIn reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. It's > slightly faster but still not that much faster than running on 16 CPU cores. 25050 [PMC free article] [Google Scholar] EDUCATION<br><br>2012 November: WHR Seminar: Seminar about Hotel Revenue, web e social Marketing at Hotel Le Le Capannelle, Roma, Italy (Nov. I would be > happy if somebody could point me out to some scripts which help me performOn Fri, Jun 27, 2008 at 9:16 PM, Gianluca Interlandi <gianluca_at_u. washington. Choose File -> Save Coordinates. edu]Reply All Saturday,. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne, Christopher G: "Re: Force field design" Messages sorted by: [ attachment ] If you are familiar with the CHARMM program, a good resource is:. 5923 Kcal/mol also we have 6. Re: Vibrational mode analysis. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. What are you trying to accomplish?Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a jsLe mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. washington. In reply to: Gianluca Interlandi: "Vibrational mode analysis" Next in thread: Richard Law: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] CHARMM does normal mode. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. washington. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small> 2011/6/29 Gianluca Interlandi <gianluca_at_u. The simulations were not performed at constant velocity > but at constant force. Gianluca Interlandi Research Assistant Professor. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. edu) Date: Thu Apr 05 2012 - 15:44:43 CDT Next message: Gianluca Interlandi: "Re: DCD" Previous message: Jérôme Hénin: "Re: changing harmonic restraints (colvars)" Next in thread: Gianluca Interlandi: "Re: DCD" Reply: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ]. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. What can be the possible cause for this or does it happens naturallyOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. at 298. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. , Thomas W. " >> Could a small damping coefficient lead to such errors? If so, what would >> be the scenarioGianluca On Sun, 30 Aug 2009, Axel Kohlmeyer wrote: > On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: >> Thank you Mike for sharing your information. Facebook gives people the power to share and makes the world more open and connected. washington. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. Eric Klavins Professor. washington. Thanks for the reply. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. edu> Date: Friday, May 4, 2007 6:53 pm Subject: Re: namd-l: query about wrapped coordinates > This script needs the information about the box size. > > Gianluca >Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. -Fatemeh On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi < gianluca_at_u. That file contains information how to run >> NAMD (and also compile it. washington. From: Gianluca Interlandi (gianluca_at_u. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. I am > using the option "wrapAll on". 26588. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). washington. From: Gianluca Interlandi (gianluca_at_u. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. washington. washington. washington. From: Gianluca Interlandi [gianluca_at_u. To: Gianluca Interlandi <gianluca_at_u. edu] Sent: Thursday, April 05, 2012 5:04 PM To: Buddhadev Maiti Cc: Jérôme Hénin; namd-l_at_ks. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. washington. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. You should simulate it in explicit water (or try one of the implicitRe: Protein in/out of box. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. 97 pN*nm = 1 Kcal/mol In reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. Michel Espinoza-Fonseca: "Re: Vibrational. From: Gianluca Interlandi (gianluca_at_u. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. MyFrom: Gianluca Interlandi (gianluca_at_u. Email:. gianluca@u. From: Gianluca Interlandi (gianluca_at_u. Sorry for posting it here, but maybe somebody might have tried it, too. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. Previous message: Gianluca Interlandi: "NAMD 2. (2010) The catch bond mechanism between von Willebrand factor. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. These are the lastIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. In the text field you can enter your atom selection, e. You can specify the nice priority in a nodelist file, for example: group main ++nice 19 host machine1 ++nice 20 host machine2 ++nice 21 host machine3> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu> > wrote: > are other people also using those GPUs? > >Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. washington. Don't take my word that this works. edu) Date: Mon Apr 11 2011 - 14:41:28 CDT Next message: Axel Kohlmeyer: "Re: Help building a desktop for namd" Previous message: Buddhadev Maiti: "(no subject)" In reply to: Axel Kohlmeyer: "Re: Help building a desktop for namd" Next in. The more tasks you have the > more frequently the CPUs need to update each other about the position > of Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Axel Kohlmeyer: "Re: Fwd: Installing NAMD on windows" Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. > > gianluca, >Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. 50% refund of amount payable if you cancel at least 7 days before check-in. You should simulate it in explicit water (or try one of the implicitCompiling NAMD 2. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. The simulations were not performed at constant velocity > but at constant force. You should simulate it in explicit water (or try one of the implicitFrom: Gianluca Interlandi <gianluca_at_u. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. edu> > wrote: > are other people also using those GPUs? > >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. Kidd, 2 Isolde Le Trong, 3 Veronika Tchesnokova, 1 Olga Yakovenko, 2 Matt J. edu> Subject: Re: namd-l: "wrapAll on" with a complex Gianluca: Using VMD with the attached script should solve that. , heavy winds caused a tree along the Burke-Gilman Trail to break in half, nearly striking a cyclist and pedestrians. I doubt that there is a way to have NAMD output theReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. From: Axel Kohlmeyer (akohlmey_at_gmail. MyOne Bedroom Apartment, Sleeps 3 - C$150 avg/night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum 2 night(s) stay Bookable directly online - Book vacation rental 11131246 with Vrbo. edu> wrote: > Hi Fatemeh, > From: Gianluca Interlandi (gianluca_at_u. edu> Cc: <namd-l_at_ks. Cancellation policy. 7b4 is that> On Feb 8, 2007, at 11:49 PM, Gianluca Interlandi wrote: > > >I have a question concerning steered molecular dynamics simulations > >(constant force and constant velocity). edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. edu>: > Dear NAMD users, > > Is it possible to perform Poisson Boltzmann calculation with NAMD? > > I have simulated the wildtype and a single-point mutant of a protein. 7 ns/day, which seems decent given the system size. From: Gianluca Interlandi (gianluca_at_u. Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. There have been over 180 downloadsReply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. On Thu, Apr 09, 2015 at 03:39:49PM -0700, Gianluca Interlandi wrote: > Dear list, > > Starting with version 1. I would be > happy if somebody could point me out to some scripts which help me performRe: Help building a desktop for namd. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Specifically, I’m testing different binding domains. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi <gianluca_at_u. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. (2010) The catch bond mechanism between von Willebrand factor and platelets investigated by molecular dynamics simulations. We are building a smaller cluster though in the lab and will test the scalability2006/9/6, Gianluca Interlandi <gianluca_at_u. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. From: John Stone (johns_at_ks. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"From: Gianluca Interlandi (gianluca_at_u. Previous message: Gianluca Interlandi: "stepspercycle" In reply to: Gianluca Interlandi: "stepspercycle" Next in thread: Gianluca Interlandi: "Re: AW: stepspercycle" Reply: Gianluca Interlandi: "Re: AW: stepspercycle" Messages sorted by: [ attachment ] No idea where you were looking, but this parameter is still fundamental for. Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. washington. I > > attach a plot of a constant velocity simulation where I'm pulling two > > proteins apart. washington. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorIn reply to: Gianluca Interlandi: "NAMD + nice" Messages sorted by: [ attachment ] Nice (process priority) is only supported in NET version of Charm++. What this rental offers. Forest, Academic Editor. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu. washington. edu> > wrote: > are other people also using those GPUs? > > > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. View the profiles of people named Gianluca Interlandi. Gianluca has 2 jobs listed on their profile. PMID: 33550613 PMCID: PMC8089038 DOI: 10. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca InterlandiHosted by Gianluca Interlandi Ask a question. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. at 298. washington. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. This school has it's > own biophysics division. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. washington. washington. Proteins. Be the first to write a review. > Auftrag von Gianluca Interlandi > Gesendet: Freitag, 13. g. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message: Lechuga, Javier: "Simulating air with NAMD" Previous message: Gianluca Interlandi: "Re: query about wrapped coordinates" Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates"In reply to: Gianluca Interlandi: "Re: Force field design" Next in thread: Axel Kohlmeyer: "Re: Force field design" Reply: Axel Kohlmeyer: "Re: Force field design" Messages sorted by: [ attachment ] On 24 July 2014 22:22, Gianluca Interlandi <gianluca_at_u. Chemistry. From: Gianluca Interlandi (gianluca_at_u. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. From: Mitchell Gleed (aliigleed16_at_gmail. You should simulate it in explicit water (or try one of the implicitNext in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. What are you trying to accomplish? Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a js Next in thread: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Gianluca: Using VMD with the attached script should solve that. In reply to: Gianluca Interlandi: "Re: namd ibverbs" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] This archive was generated by hypermail 2. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). edu) Date: Wed Aug 05 2009 - 13:19:25 CDT Next message: Gianluca Interlandi: "Re: SMD output : which col represents force, second or last" Previous message: David Tanner: "Re: SMD output : which col represents force, second or last" In. I got 0. Languages: English, Spanish, Italian. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. washington. (did you see if any hunk failed?)Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. Re: How to unsubscribe ? From: Gianluca Interlandi (gianluca_at_u. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. washington. edu> wrote: > Hi Fatemeh, >> On Wed, Dec 12, 2012 at 12:26 PM, Gianluca Interlandi <gianluca_at_u. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. I was getting 2. Abstract. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallmargin errors. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the. washington. washington. But, using the PBC my protein is continuous. Re: external force. Biochemistry. " Messages sorted by: [ attachment ] On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: > Thank you Mike for sharing your information. edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the Abmer force field Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. edu> > wrote:Re: Help building a desktop for namd. MyGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. I empolyed PBC condition with wraping water and wraping all options on. From: Gianluca Interlandi (gianluca_at_u. RE: Force field design. edu Subject: Re: namd-l: DCD Load your psf+dcd into VMD. washington. Usually, this > is > written in the dcd file if you specified "DCDUnitCell yes" in your > NAMD > config file. Re: Abe versus Lincoln. Previous studies. washington. edu) Date: Wed May 16 2007 - 14:43:41 CDT Next message: Ayşe Özlem Sezerman: "System charge" Previous message: Peter Freddolino: "Re: Minimization" In reply to: Viswanadham Sridhara: "How to unsubscribe ?" Messages. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. rtf" and "par_all36_prot. washington. >> >> According to your banchmarks, it looks like the less expensive GTX285 >> (around 300$) performs better than a Tesla C1060 which is 4 times more >> expensive. 478 KJ/mol = 0. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. 1002/prot. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. washington. I know the lack of treatment of the hydrophobic part but the point here is the different results for same implicit solvent model. washington. washington. Search for: Main Menu. washington. My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. washington. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. edu Search for more papers by this author> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. unizh. Spaces. At the point of breaking the temperature raises of a few> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. Biochemistry. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. washington. VMD-L Mailing List. washington. edu) Date: Tue Jul 15 2014 - 22:32:35 CDT Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne,. Interlandi G. Next in thread: Gianluca Interlandi: "Re: NAMD 2. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca InterlandiReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. From: Gianluca Interlandi (gianluca_at_u. I want to simulate a protein > attached to mannose. Re: Protein in/out of box. 15 K 1 KT = 2. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. com) Date: Wed Aug 27 2014 - 22:13:06 CDT Next message: Gianluca Interlandi: "Re:" Previous message: Douglas Houston: "Re: AW: Using nodelist file causes namd to hang" Next in thread: Gianluca Interlandi: "Re:" Reply: Gianluca Interlandi: "Re:" Messages sorted by: [. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. washington. Whitfield, 2 Esther Bullitt, 4 Ronald E. You should simulate it in explicit water (or try one of the implicitOn Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread:. edu]Reply All Saturday,. washington. washington. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. 7b1 - effects of configuration parameters and hardware. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. washington. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. I’m working in Research Assistant Professor Gianluca Interlandi’s research lab, and I study the behavior of the Von Willebrand factor (VWF), which is a plasma protein that recruits platelets to the site of blood vessel injury. I would like to erase Windows and install Leap 42. washington. edu on behalf of Gianluca Interlandi [gianluca_at_u. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. washington. washington.