[gmx-users] Re: Looking for GPU benchmarks

OK. Which version / branch / revision should I use then ? Thanks. -- View this message in context: http://gromacs.5086.n6.nabble.com/Looking-for-GPU-benchmarks-tp5000377p5000609.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@g

Re: [gmx-users] Re: Cross-correlation maps

Hey, In addition to Newton's cradle, there's also Columbus' egg. To make it stand, you smash it slightly, pressing one end. If you do PCA on that, you'll find a collective motion involving both the smashed end as well as the opposite, unscathed end. That accounts for the greater part of the global

Re: [gmx-users] Re: Cross-correlation maps

On 28/08/2012 4:09 PM, James Starlight wrote: Mark, Thanks for explanation! 2012/8/27, Mark Abraham : Did you construct a correlation matrix from side chain atoms? Yes, and there is some degree of correlation between adjacent side chains but lack of any cooperativety between distant side-ch

Re: [gmx-users] Re: Cross-correlation maps

Mark, Thanks for explanation! 2012/8/27, Mark Abraham : > Did you construct a correlation matrix from side chain atoms? Yes, and there is some degree of correlation between adjacent side chains but lack of any cooperativety between distant side-chains. In comparison in that protein there were

Re: [gmx-users] Re: Cross-correlation maps

On 28/08/2012 3:09 PM, James Starlight wrote: Hi Tsjerk! Normally during analysis of the MD trajectory I've observed frequent side-chain fluctuations (ps timescale) cased by the temperature motion of the atoms as well as larger-scale backbone motions ( on the ns time). The ps side-chains motio

Re: [gmx-users] Re: Cross-correlation maps

Hi Tsjerk! Normally during analysis of the MD trajectory I've observed frequent side-chain fluctuations (ps timescale) cased by the temperature motion of the atoms as well as larger-scale backbone motions ( on the ns time). The ps side-chains motions are known to especially increase total enthro

[gmx-users] mdrun_gpu on NVidia Quadro 2000

Hi, I was wondering if the numbers I get are reasonable while running the DHFR benchmark at: http://www.gromacs.org/Documentation/Installation_Instructions/GPUs As you can see, CPU performance is quite good, but GPU performance is really bad compared with results on that page for other cards (Tes

Re: [gmx-users] Problem with incorrect GB-Polarization Energy Value

On 28/08/2012 2:33 AM, jesmin jahan wrote: Dear All, I am using Gromacs 4.5.3 for GB-Polarization Energy Calculation. As I am not interested to any other energy terms right now, I have set all the non-bonded parameters to 0. I am also calculating GB polarization energy using other available Mol

Re: [gmx-users] Question about Multi-level parallelization: MPI and OpenMP

Okay Mark, Thanks!. Best Regards, Jesmin On Mon, Aug 27, 2012 at 6:15 PM, Mark Abraham wrote: > On 28/08/2012 2:40 AM, jesmin jahan wrote: >> >> Dear Gromacs Users, >> >> I have two questions about the multi-level parallelism of Gromacs. >> >> http://www.gromacs.org/Documentation/Acceleration_an

Re: [gmx-users] Question about Multi-level parallelization: MPI and OpenMP

On 28/08/2012 2:40 AM, jesmin jahan wrote: Dear Gromacs Users, I have two questions about the multi-level parallelism of Gromacs. http://www.gromacs.org/Documentation/Acceleration_and_parallelization?highlight=verlet#GPU_acceleration 1. Is this feature is only supported by Gromacs 4.6? Or we ca

Re: [gmx-users] Incorrect bond in top file

On 8/27/12 3:03 PM, Shima Arasteh wrote: OK, I checked the bonds section of top, there is no bond between CN and HN. Thanks for it. But there is a new problem. I passed the steps for simulation the protein in water, up to the EM step. I ran grompp and then mdrun to do energy minimization

Re: [gmx-users] Re: Cross-correlation maps

Hi James, Correlation is covariance normalized to variance. So you'll need the covariance matrix anyway. But what exactly due you mean with the loss of information, which you could solve with correlations? Cheers, Tsjerk On Aug 27, 2012 4:01 PM, "James Starlight" wrote: Mark, Is there any wa

Re: [gmx-users] Incorrect bond in top file

OK, I checked the bonds section of top, there  is no bond between CN and HN.  Thanks for it. But there is a new problem. I passed the steps for simulation the protein in water, up to the EM step. I ran grompp and then mdrun to do energy minimization. I see the protein broken. As you said i

Re: [gmx-users] Incorrect bond in top file

On 8/27/12 2:35 PM, Shima Arasteh wrote: Please take a look at the .top file generated: 1 C 1 FVAL CN 1 0.357 12.011 ; qtot 0.357 2 HA 1 FVAL H1 20.1 1.008 ; qtot 0.457 3 O 1 FVAL

Re: [gmx-users] Incorrect bond in top file

Please take a look at the .top file generated: 1  C  1   FVAL CN  1  0.357 12.011   ; qtot 0.357 2 HA  1   FVAL H1  2    0.1  1.008   ; qtot 0.457 3  O  1   FVAL ON  3  -0.51 15.999   ; qtot -0.0

Re: [gmx-users] Incorrect bond in top file

 Yes. So what's the problem?! Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Monday, August 27, 2012 10:45 PM Subject: Re: [gmx-users] Incorrect bond in top file On 8/27/12 1:31 PM, Shima Arasteh wrote: > :D > Hope so (

Re: [gmx-users] Elastic network model -building

On Aug 27, 2012, at 7:14 PM, mohan maruthi sena wrote: Hi, Thanks for your reply. I have written a script which gives the atoms with in certain cut-off distance from specified atom. I have added this to topology , the problem is that it creates topology from pdb but not the other way. Not

Re: [gmx-users] Incorrect bond in top file

On 8/27/12 1:31 PM, Shima Arasteh wrote: :D Hope so ( for your caps lock )! ;) Thanks, I'm happy! The relevant rtp file: [ FVAL ] [ atoms ] CNC 0.3570 ONO-0.511 H1HA0.1002 NNH1-0.4233 HNH0.3334 CA

Re: [gmx-users] Force Field Choice

On 8/27/12 1:32 PM, Marcelo Depolo wrote: Dear all, Is there a consensus on force field choice? I read in this group, people suggesting compare experimental data and simulation data. But in case of there's none experimental data about structural data, what to do? There was a discussion abo

Re: [gmx-users] Incorrect bond in top file

:D Hope so ( for your caps lock )! ;) Thanks, I'm happy! The relevant rtp file: [ FVAL ]  [ atoms ]     CN    C     0.357    0     ON    O    -0.51    1     H1    HA    0.100    2     N    NH1    -0.423    3     HN    H    0.333    4     CA    CT1    0.034    5     HA    HB    0.09    6     CB  

[gmx-users] Force Field Choice

Dear all, Is there a consensus on force field choice? I read in this group, people suggesting compare experimental data and simulation data. But in case of there's none experimental data about structural data, what to do? I apologize previously the silly doubt. Best regards! -- Marcelo Depólo P

Re: [gmx-users] Elastic network model -building

Hi, Thanks for your reply. I have written a script which gives the atoms with in certain cut-off distance from specified atom. I have added this to topology , the problem is that it creates topology from pdb but not the other way. I use first pdb2gmx -f pdb -o gro -p top (command to generate

Re: [gmx-users] Elastic network model -building

There is no script generating an elastic network in Gromacs. You could use the script that we developed in the context of the Martini CG model (cgmartini.nl) but it would be certainly easier for you to simply write a script that would rad the Clapha coordinates and define the ones that are

[gmx-users] Question about Multi-level parallelization: MPI and OpenMP

Dear Gromacs Users, I have two questions about the multi-level parallelism of Gromacs. http://www.gromacs.org/Documentation/Acceleration_and_parallelization?highlight=verlet#GPU_acceleration 1. Is this feature is only supported by Gromacs 4.6? Or we can get it in 4.5.3 also? 2. In Gromacs 4.5.3,

[gmx-users] Problem with incorrect GB-Polarization Energy Value

Dear All, I am using Gromacs 4.5.3 for GB-Polarization Energy Calculation. As I am not interested to any other energy terms right now, I have set all the non-bonded parameters to 0. I am also calculating GB polarization energy using other available Molecular Dynamic Packages and doing a comparati

Re: [gmx-users] Incorrect bond in top file

On 8/27/12 11:41 AM, Shima Arasteh wrote: Dear users, [ Especially dear Justin ( please don't shout at me! ) ], I haven't, and won't. I keep my caps lock off ;) Hopefully no one gets the impression that I have done otherwise... As I have described it many times, I defined a new re

[gmx-users] Incorrect bond in top file

Dear users, [ Especially dear Justin ( please don't shout at me! ) ], As I have described it many times, I defined a new residue named FVAL in aminoacids.rtp of the force field ( CHARMM36). The first step is "generating top file". When I ran the command of pdb2gmx, the top file is generated

[gmx-users] RE: Looking for GPU benchmarks

Hi, Thanks for your answer. The thing is that I am a benchmarker and I have no knowledge of the physics behind GROMACS. My goal is to demonstrate the interest (or not) in using GPUs for a customer test case. So my idea would be to do one run using the CPU only version of GROMACS, then m

Re: [gmx-users] Re: Looking for GPU benchmarks

Which system did you run? What settings? A few tips: - Use CUDA 4.2 (5.0 on Kepler); - Have at least 10-20k atoms/GPU (and more to get peak GPU performance); - Use the shortest cut-off possible to allow CPU-GPU load balancing; - Due to initial domain-decomposition/parallelization overhead, scaling

Re: [gmx-users] NPT equilibration in KALP15-DPPC

On 8/27/12 10:27 AM, Shima Arasteh wrote: I removed the water molecules located between carbon chains of lipids. Then updated the top file. Should the atom numbers of "nvt.gro" be changed? This is not clear for me. I updated the nvt.gro, Running: grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p to

Re: [gmx-users] NPT equilibration in KALP15-DPPC

I removed the water molecules located between carbon chains of lipids. Then updated the top file. Should the atom numbers of "nvt.gro"  be changed? This is not clear for me. I updated the nvt.gro, Running: grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr but it gives

Re: [gmx-users] Re: Cross-correlation maps

Mark, Is there any way to calculate such cross-correlations without calculation of the covariance matrix ( from the MD trajectory indirectly) ? I've noticed that after processind of my trajectory with PCA method some dynamics ( e.g fluctuations of the side-chains) are lost even when I've analysed

Re: [gmx-users] GROMACS command for energy calculation

On 27/08/2012 8:32 PM, Acoot Brett wrote: Hi Mark, Then MAP file has the ability to recognize the groups saved in the index file, which is in the same folder as the MDP file? I have no idea what you mean. Make the index groups in the index file and use them with commands like grompp -n your

Re: [gmx-users] Broken protein after EM

On 8/27/12 8:27 AM, Shima Arasteh wrote: Dear gmx users, I'm simulating a protein in water. I ran these commands: 1.pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter 2.editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic 3.genbox -cp monomer_newbox.gro -cs spc216.gro -o mono

[gmx-users] Broken protein after EM

Dear gmx users, I'm simulating a protein in water. I ran these commands: 1.pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter 2.editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic 3.genbox -cp monomer_newbox.gro -cs spc216.gro -o monomer_solv.gro -p topol.top 4.grompp -f ions.md

[gmx-users] Variation of box angles - regd

Dear GMX users, I want to see how box angles are varying during my simulations, I have no idea where box angles will be stored in gromacs output files and how to extract them . Can anybody please help me in this regard. Thank you in advance Regards, Ram

Re: [gmx-users] Re: Looking for GPU benchmarks

On 8/27/12 7:31 AM, Mathieu38 wrote: I have tried the basic approcah of taking some of the input files that are provided with the sources of Gromacs or on the website, and adding the line cutoff-scheme = Verlet in the grompp.mdp file However, I have not find a case where use of GPUs (2 MPI T

[gmx-users] Re: [gmx-developers] Mails rejected with "The message's content type was not explicitly allowed"

Hi, There was an issue with /multipart/ missing from the allowed mime types. Now HTML mails should be also accepted. Rossen On 7/5/12 3:24 PM, Rossen Apostolov wrote: Dear all, Recently the Gromacs mailing lists have been used for sending spam and viruses, and thus now only plain text mess

[gmx-users] Re: Looking for GPU benchmarks

I have tried the basic approcah of taking some of the input files that are provided with the sources of Gromacs or on the website, and adding the line cutoff-scheme = Verlet in the grompp.mdp file However, I have not find a case where use of GPUs (2 MPI Tasks, 4 OpenMP Threads per MPI tasks

[gmx-users] test, please ignore

test *test* /test/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe re

Re: [gmx-users] overlaps atoms during solvation(genbox)

On 8/27/12 6:47 AM, Vasumathi Velachi wrote: Hi I new in using Gromacs. I used genbox to solvate my solute(gold+thiols), when I am doing so the resultant pdb have the overlaps between water molecule and gold. This overlaps is due to the missing information for gold in the file "vdwdradii.dat"

[gmx-users] overlaps atoms during solvation(genbox)

Hi I new in using Gromacs. I used genbox to solvate my solute(gold+thiols), when I am doing so the resultant pdb have the overlaps between water molecule and gold. This overlaps is due to the missing information for gold in the file "vdwdradii.dat". In order to avoid the overlaps shall i incr

Re: [gmx-users] GROMACS command for energy calculation

On 8/27/12 6:32 AM, Acoot Brett wrote: Hi Mark, Then MAP file has the ability to recognize the groups saved in the index file, which is in the same folder as the MDP file? Any group specified in the .mdp file must be recognized by grompp (in the case of default groups) or otherwise suppli

Re: [gmx-users] GROMACS command for energy calculation

Hi Mark,   Then MAP file has the ability to recognize the groups saved in the index file, which is in the same folder as the MDP file? Acoot - Original Message - From: Mark Abraham To: Discussion list for GROMACS users Cc: Sent: Monday, 27 August 2012 8:00 PM Subject: Re: [gmx-users

Re: [gmx-users] NPT equilibration in KALP15-DPPC

On 8/27/12 2:30 AM, Shima Arasteh wrote: Hi, After the NPT mdrun, I visulized the npt.gro. I need to know if this npt.gro is the final result of equilibration? From mdrun -h: "The structure file (-c) contains the coordinates and velocities of the last step." I see 2,3 water molecules

Re: [gmx-users] GROMACS command for energy calculation

On 27/08/2012 7:42 PM, Acoot Brett wrote: Dear Justin, For example, I want to calculate the energy between residue 50 and residue 100, then I create an index file (A), then in the MDP file I will insert energygryp=A (with indec file extension or not?), then do the rerun, am I right? An index

Re: [gmx-users] GROMACS command for energy calculation

Dear Justin,   For example, I want to calculate the energy between residue 50 and residue 100, then I create an index file (A), then in the MDP file I will insert energygryp=A (with indec file extension or not?), then do the rerun, am I right?   Cheers,   Acoot     - Original Message -