[gmx-users] RE:Interaction Energy

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs <lloyd.riggs at gmx.ch 
> <mailto: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 <mailto:jalemkul at vt.edu>>
>     Subject: Re: [gmx-users] Interaction energy
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <4E9D57F3.10905 at vt.edu <mailto: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>
>      > <mailto: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?
>  

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

-- 
========================================

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

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