Re: [gmx-users] Running MD only for selected part of molecule

Hi Justin, Thanks for your reply... and apologies for asking you again. If I want to keep a part of my molecule fix, say part out of 12 angstrom radius from the ligand and also want to make avoid energy calculation for the same, (using energy_excl) Do I need to mention the separate group for that

Re: [gmx-users] Running MD only for selected part of molecule

Dear Justin, Thanks for your reply.. But I am not getting how and where should I give the option of energy_excl. For freezing a part of molecule ? what are the other checks to be done for the same ? With Thanks, Vivek 2008/10/14 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote:

Re: [gmx-users] Running MD only for selected part of molecule

vivek sharma wrote: Dear Justin, Thanks for your reply.. But I am not getting how and where should I give the option of energy_excl. For freezing a part of molecule ? In the .mdp file. what are the other checks to be done for the same ? I don't know what you're asking. -Justin With

Re: [gmx-users] Running MD only for selected part of molecule

Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same. But, I have seen that the part of the molecule I kept for PR is still having some motion, how can I

Re: [gmx-users] Running MD only for selected part of molecule

vivek sharma wrote: 2008/10/14 Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] vivek sharma wrote: Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for

Re: [gmx-users] Running MD only for selected part of molecule

2008/10/14 Justin A. Lemkul [EMAIL PROTECTED] vivek sharma wrote: Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same. But, I have seen that

Re: [gmx-users] Running MD only for selected part of molecule

vivek sharma wrote: Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same. But, I have seen that the part of the molecule I kept for PR is still

Re: [gmx-users] Running MD only for selected part of molecule

Hi Justin, I tried the genpr for generating the posre.itp, but it is taking only a single residue while I want to restrict a number of residue for the mdrun. Please suggest me the way out. Procedure followed: generated gro using pdb2gmx generated box using editconf add water using

Re: [gmx-users] Running MD only for selected part of molecule

Hi, On Oct 10, 2008, at 12:46 PM, Justin A. Lemkul wrote: I want to run MD over a part of my molecule , for few residues only (not the whole molecule). Can I do it using GROMACS ? I searched for the online documentation and mailing list, but unable to get appropriate information. If

Re: [gmx-users] Running MD only for selected part of molecule

Thanks Justin, My goal is to keep certain part fixed and move only a few of the residues (case is like providing flexibility to the site of interest only). SO , do I need to specify the residue using some index file ? or is there some other way to specify the part of molecule for position

Re: [gmx-users] Running MD only for selected part of molecule

Justin A. Lemkul wrote: vivek sharma wrote: Thanks Justin, My goal is to keep certain part fixed and move only a few of the residues (case is like providing flexibility to the site of interest only). SO , do I need to specify the residue using some index file ? or is there some other

Re: [gmx-users] Running MD only for selected part of molecule

hI justin, Thanks for your response. do I need to specify the index file(for residue that I want to keep fix during MD) during GROMPP or just including the psre.itp in topology is enough for the purpose ? With Thanks, Vivek 2008/10/10 Justin A. Lemkul [EMAIL PROTECTED] Justin A. Lemkul

Re: [gmx-users] Running MD only for selected part of molecule

Hi justin, My apologies for asking you so many small queries. Can you suggest any good tutorial or reference that talks about this issue of running MD over a selected part of molecule. With Thanks, Vivek 2008/10/10 vivek sharma [EMAIL PROTECTED] hI justin, Thanks for your response. do I

Re: [gmx-users] Running MD only for selected part of molecule

vivek sharma wrote: hI justin, Thanks for your response. do I need to specify the index file(for residue that I want to keep fix during MD) during GROMPP or just including the psre.itp in topology is enough for the purpose ? No; you just need it to pass to genpr. Please remember to copy

Re: [gmx-users] Running MD only for selected part of molecule

vivek sharma wrote: Hi justin, My apologies for asking you so many small queries. Can you suggest any good tutorial or reference that talks about this issue of running MD over a selected part of molecule. If you're using PR, all you're doing is position-restrained dynamics. -Justin

[gmx-users] Running MD only for selected part of molecule

Hi there, I want to run MD over a part of my molecule , for few residues only (not the whole molecule). Can I do it using GROMACS ? I searched for the online documentation and mailing list, but unable to get appropriate information. If somebody has already tried such things earlier, please

Re: [gmx-users] Running MD only for selected part of molecule

vivek sharma wrote: Hi there, I want to run MD over a part of my molecule , for few residues only (not the whole molecule). Can I do it using GROMACS ? I searched for the online documentation and mailing list, but unable to get appropriate information. If somebody has already tried such

Re: [gmx-users] Running MD only for selected part of molecule

You might want to try Simbody (simtk.org). This will allow you to rigidify any part or parts of the molecule you choose. As a bonus, you will not spend resources computing intramolecular interactions in the rigidified regions. Sam On Oct 10, 2008, at 6:10 AM, Justin A. Lemkul wrote: