On Tue, Oct 18, 2011 at 2:50 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > >> >> >> On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs <lloyd.ri...@gmx.ch <mailto: >> lloyd.ri...@gmx.ch>> wrote: >> >> Message: 1 >> Date: Tue, 18 Oct 2011 06:41:55 -0400 >> From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> Subject: Re: [gmx-users] Interaction energy >> To: Discussion list for GROMACS users <gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>**> >> Message-ID: <4e9d57f3.10...@vt.edu <mailto:4e9d57f3.10...@vt.edu>**> >> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> >> Steven Neumann wrote: >> > >> > >> > On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> > <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> > >> > >> > >> > Steven Neumann wrote: >> > >> > Dear Gmx Users, >> > I would like to calculate the interaction energy (LJ and >> > electrostatic) between each residue and my ligands (10 >> ligands >> > in the system). I would like to see what is the >> contribution of >> > electrostatic and vdW interactions between ligand and >> each of my >> > residue. I thought to use g_energy and specify each of my >> > residues in index files but it is not possible. Will you >> suggest >> > how to do this? >> > >> > >> > >> > For such information, you have to specify these groups as >> energygrps >> > in the .mdp file. You can rerun the trajectory using mdrun >> -rerun >> > and a new .tpr file specifying these groups, but depending on >> the >> > output frequency, the result may not be as accurate as you'd >> like. >> > >> > -Justin >> > >> > >> > Thank you Justin. Now I have two groups sepcified in my mdp file: >> > >> > energygrps = Protein LIG >> > >> > How can I specify each residue of my protein separately and each >> ligand? >> > In my md.gro file I have residues: >> > >> > 91GLY 92TYR ..... 161LIG 162LIG... >> > >> > >> > Will it be correct like this >> > >> > energygrps = 91GLY 92 TYR ... 161LIG 162LIG... >> > >> >> No. The names must correspond to valid groups in an index file. >> >> > If yes, will this simulation take longer? Thank you >> >> Perhaps, but certainly your energy file will be considerably larger. >> >> -Justin >> >> > >> > Steven >> > >> > >> > >> > >> > >> >> >-- >> >=============================**=========== >> >> Dear Steven, >> >> I did the following, but like Justin mentioned the files get large. >> Basically, I made a very complex ndx file from the beggining. I >> have the whole proteins and peptides involved, then a series of >> loops, and protein minus loop, and then individual amino acids and >> protein minus the amino acids. Basically every time you make the >> ndx for a particular amino acid/chain/loop you also have to generate >> the ndx for the rest of your protein minus what you were looking at. >> Otherwise you run out of groups to assign, and will start getting >> "residue or atom in multiple groups" when it is referenced more than >> one time. >> >> This might not be necessary in your case, but lets you divie up >> energy contributions easier, although multiple re-runs using varied >> indexes might be necessary, ie for the sum total, then varied parts, >> etc... >> >> At least that is a suggestion from my experience.. >> >> Freundlichen Grüsse >> >> Stephan Watkins >> -- >> NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! >> Jetzt informieren: >> http://www.gmx.net/de/go/**freephone<http://www.gmx.net/de/go/freephone> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org>>. >> >> >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> Thank you Stephan! I have faced the problem you mentioned: >> Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 3) >> So as I understood what you have written I should specify in my >> INDEX.ndx: >> [r_91] - residue 91 >> 1 2 3.... 7 >> [Protein-r91] - Protein without residue 91 >> 8 9 10 11... 382 >> [r_92] - resideu 92 >> 8 9 10 11...17 >> [Protein-r92] - Protein without residue 92 >> 1 2..7 18 19 20...38 >> etc. etc. >> And the same with ligands but substracting from my [System] group? >> >> > > This is not a correct approach, per the fatal error. If you want to > monitor energies involving different residues, the only requirement is that > those residues be in their own distinct groups, i.e.: > > energygrps = r_91 r_92 r_93 ... Ligand > > The energy groups cannot be redundant. What Stephan was suggesting is that > you cannot, for instance, specify: > > energygrps = Protein r_91 r_92 ... > > because "Protein" encompasses residues 91, 92, etc. You can, however, > specify energygrps as in my first example, such that the whole "Protein" > group is not one of the energygrps. If you want energies involving those > residues, you have to do as Stephan suggested and create an "incomplete" > protein group that excludes the residues that you want to specifically > analyze. > > -Justin > Thank you both!!!! Steven > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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