On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs <lloyd.ri...@gmx.ch> wrote:
> Message: 1 > Date: Tue, 18 Oct 2011 06:41:55 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Interaction energy > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <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>> 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 > -- > gmx-users mailing list gmx-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 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 > 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? Then [Ligand] - all Ligands atoms [Protein] - all Protein atoms [Water] - all Water atoms. Please let me whether I am correct. Did such simulation take much longer? I run 100ns simulations for 2 days on the cluster with specified energy groups for Protein and Ligand only. My system consists of app. 4000 atoms only (water+protein+ligands). Thank you, Steven
-- gmx-users mailing list gmx-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 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