Re: [gmx-users] steered pulling code on ligand-receptor complex

2012-10-31 Thread Jianguo Li
If you position restraint the receptor or only use several residues at the binding site, in both cases you limit your sampling to a small part of the phase space and the PMF may not be accurate, since the receptor may undergo conformational change upon ligand binding. Cheers --Jianguo - O

[gmx-users] fraction of native contacts calculation

2012-10-31 Thread bipin singh
Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. *-- --- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

Re: [gmx-users] Error in npt run - box size/ triclinic skew factor

2012-10-31 Thread Justin Lemkul
On 10/30/12 4:23 PM, mtso wrote: When trying to do an npt run, I get the fatal error: The X-size of the box (3.999511) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.00). I should mention, I'm brand new to using

Re: [gmx-users] Why potential energy not in negative value?

2012-10-31 Thread Justin Lemkul
On 10/31/12 4:10 AM, Nur Syafiqah Abdul Ghani wrote: Dear All, Currently I'm doing the minimization part for my solvent which is hexafluoroisopropanol with water. I'm packing them with packmol then use the forcefield gromos96. Now by using the command grompp -f em1.mdp -c minimize_301012.gro

Re: [gmx-users] fraction of native contacts calculation

2012-10-31 Thread Justin Lemkul
On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code t

[gmx-users] time-block analysis

2012-10-31 Thread Christopher Neale
Technically, in order to show that your simulation has reached complete convergence, you would need to show that every type of data has converged. Obviously nobody does this. You should start with looking at the convergence of any data type that you analyze in any other way. i.e. if you show a h

[gmx-users] Re: Error in npt run - box size/ triclinic skew factor

2012-10-31 Thread mtso
Thanks Justin, We're using the tutorial, and those .mdp files as a starting point but actually running the simulations on the protein PDB ID 2LFM, without adding a ligand for now, and modifying the .mdp files as necessary. -- View this message in context: http://gromacs.5086.n6.nabble.com/E

Re: [gmx-users] Re: Error in npt run - box size/ triclinic skew factor

2012-10-31 Thread Justin Lemkul
On 10/31/12 10:23 AM, mtso wrote: Thanks Justin, We're using the tutorial, and those .mdp files as a starting point but actually running the simulations on the protein PDB ID 2LFM, without adding a ligand for now, and modifying the .mdp files as necessary. Just make sure whatever changes you

[gmx-users] testing Gromacs 4.6 (git version) on GPUs

2012-10-31 Thread Susan Chacko
Hi all, I wanted to test the built-in support in Gromacs 4.6 (non-OpenMM) for GPUs. I downloaded the latest git version and it built successfully, appears to link the right CUDA libraries etc. I tried testing it with the Gromacs GPU benchmark suite (http://www.gromacs.org/@api/deki/files/128/=

[gmx-users] Re, density

2012-10-31 Thread Christopher Neale
Dear Ali: I am not sure what ecenter is, it looks like it might be the position to which the user wants to set the center? In any event, it doesn't mater for this modification. I did not write the center_x() function, it is a standard part of gmx_trjconv.c What I did was to copy center_x() to

[gmx-users] time-block analysis

2012-10-31 Thread Christopher Neale
Leila, I provided 2 good references to answer your question earlier. If you can't be bothered to read about it, then the answer is yes, it is a good method. Looking at your other questions, I think that it is time for you to look at those references and learn more about block averaging and conve

[gmx-users] About Doubt in Lipid protein Solvation

2012-10-31 Thread vidhya sankar
Dear Justin Thank you For your Previous Kind Reply    I am following your Lipid-protein Tutorial  for My system   I  Gave The Following Commands As Quoted in your Tutorial Also I Have Suitably Edited The Topology As in

Re: [gmx-users] About Doubt in Lipid protein Solvation

2012-10-31 Thread Justin Lemkul
On 10/31/12 11:45 AM, vidhya sankar wrote: Dear Justin Thank you For your Previous Kind Reply I am following your Lipid-protein Tutorial for My system I Gave The Following Commands As Quoted in your Tutorial A

Re: [gmx-users] testing Gromacs 4.6 (git version) on GPUs

2012-10-31 Thread Roland Schulz
Hi, you can use the tpr files from the tgz if you use the non-implicit "solv" (preferable PME) test. Roland On Wed, Oct 31, 2012 at 10:37 AM, Susan Chacko wrote: > > Hi all, > > I wanted to test the built-in support in Gromacs 4.6 (non-OpenMM) for GPUs. > I downloaded the latest git version an

Re: [gmx-users] testing Gromacs 4.6 (git version) on GPUs

2012-10-31 Thread Susan Chacko
Thank you! Yes, I am able to run the 'dhfr-solv-PME.bench' benchmark with mdrun -s topol.tpr -testverlet and it seems to be using the GPUs as well: --- 2 GPUs detected: #0: NVIDIA Tesla M2050, compute cap.: 2.0, ECC: yes, stat: compatible #1: NVIDIA Tesla M2050, compute cap.: 2.0, ECC: yes,

[gmx-users] Re: Error in npt run - box size/ triclinic skew factor

2012-10-31 Thread mtso
>Just make sure whatever changes you are making are correct for the chosen force >field and algorithms. If you're having problems with NPT, you can always switch >to the Berendsen algorithm for pressure coupling before returning to >Parrinello-Rahman for data collection. -Justin Thanks for

Re: [gmx-users] Re: Error in npt run - box size/ triclinic skew factor

2012-10-31 Thread Justin Lemkul
On 10/31/12 12:38 PM, mtso wrote: Just make sure whatever changes you are making are correct for the chosen force field and algorithms. If you're having problems with NPT, you can always switch to the Berendsen algorithm for pressure coupling before returning to Parrinello-Rahman for da

[gmx-users] What exactly is the artifact caused by setting refcoord_scaling=no with position restraint

2012-10-31 Thread Christopher Neale
I've asked the same question myself and would also like to know. That said, there seems to be no issue if you set refcoord_scaling=com. According to the manual, this does not give artefacts (whatever they are) and also does not change your restraint positions (as refcoord_scaling=all does). Sor

Re: [gmx-users] Freeze group atoms changing position

2012-10-31 Thread Alex Marshall
As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I

[gmx-users] Freeze group atoms changing position

2012-10-31 Thread Christopher Neale
No need to rename... just make an .ndx group. -- original message -- As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water mode

Re: [gmx-users] Freeze group atoms changing position

2012-10-31 Thread Alex Marshall
Chris, is that for freeze groups or position restraints? On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > No need to rename... just make an .ndx group. > > -- original message -- > > As I understand it, position restraints for an atom are set in the topo

Re: [gmx-users] Freeze group atoms changing position

2012-10-31 Thread Justin Lemkul
On 10/31/12 3:55 PM, Alex Marshall wrote: Chris, is that for freeze groups or position restraints? I will assume Chris was referring to the restraint method - you need an index file for creating the position restraint .itp file using genrestr. It will save you a ton of time over doing it

[gmx-users] Freeze group atoms changing position

2012-10-31 Thread Christopher Neale
Well, I thought that it would work for for freeze groups, and that is what I intended to say. I've used freeze groups before, but don't have tonnes of experience with them. The gromacs mdp options page reads as if it should work ( http://manual.gromacs.org/online/mdp_opt.html#neq ), but if Just

Re: [gmx-users] Freeze group atoms changing position

2012-10-31 Thread Justin Lemkul
On 10/31/12 4:21 PM, Christopher Neale wrote: Well, I thought that it would work for for freeze groups, and that is what I intended to say. I've used freeze groups before, but don't have tonnes of experience with them. The gromacs mdp options page reads as if it should work ( http://manual.g

[gmx-users] Freeze group atoms changing position

2012-10-31 Thread Christopher Neale
makes sense. -- original message -- On 10/31/12 4:21 PM, Christopher Neale wrote: > Well, I thought that it would work for for freeze groups, and that is what I > intended to say. I've used freeze groups > before, but don't have tonnes of experience with them. The gromacs mdp > options page rea

Re: [gmx-users] g_rdf

2012-10-31 Thread Justin Lemkul
On 10/31/12 4:56 PM, Ali Alizadeh wrote: Dear All users I have a system that contains water , methane and propane in 240 k and 300 bar, My simulation box is rectangular . Water film is in middle of my box. Methane and propane is around it. My simulation box is symmetric, 1- I used g_rdf pr

[gmx-users] g_rdf

2012-10-31 Thread Christopher Neale
Dear Ali: I don't think that you are re-posting the same question often enough. Perhaps you should repost more often? 4 identical posts in 5 hours might not be enough to get a reply Seriously though, we all saw your message. Chris. -- original message(s) -- I have a system that conta

[gmx-users] Gmx Hessian

2012-10-31 Thread Yao Yao
hi Gmxers, is the Hessian matrix unit in gmx is ps^(-2), or J *mol^(-1) nm^(-2)? thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before postin

Re: Re: [gmx-users] steered pulling code on ligand-receptor complex

2012-10-31 Thread 范聪
Thank you so much! > -原始邮件- > 发件人: "Jianguo Li" > 发送时间: 2012年10月31日 星期三 > 收件人: "Discussion list for GROMACS users" > 抄送: > 主题: Re: [gmx-users] steered pulling code on ligand-receptor complex > > If you position restraint the receptor or only use several residues at the > binding site