[gmx-users] RE:Interaction Energy
s.neumann08 at gmail.com
Tue Oct 18 15:44:56 CEST 2011
On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
> Message: 1
> Date: Tue, 18 Oct 2011 06:41:55 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Interaction energy
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E9D57F3.10905 at 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 <jalemkul at vt.edu
> > <mailto:jalemkul at 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.
> > 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 at gromacs.org
> 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-request at 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
And the same with ligands but substracting from my [System] group?
[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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users