[gmx-users] RE:Interaction Energy

[Steven Neumann]

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.
>
> -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
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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
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