[gmx-users] energy_terms

[Mark Abraham]

On 18/12/2011 3:56 AM, balaji nagarajan wrote:
>
> Dear Users !
>
> I can print the values of the bonded and non bonded energy terms of 
> the protein and the water ,
>
> I have used the group option ,
>
> I want to know the bonded contribution only from the protein ,
> in case of the torsion energy term it is only for the protein ,
>
> The bond distance and the bond angle , the contribution from the water 
> is also there , so how one can get these
> terms for protein alone .

You can't do this during the original simulation, but you can take a 
completed simulation and use tpbconv on the .tpr and trjconv on the 
trajectory file to extract the same subset of atoms from each. Now mdrun 
-rerun on those two partial files can give you the bonded energies of 
whatever interests you. Whether that bond energy means anything is 
another matter.

Mark

>
> thanks in advance
>
> ------------------------------------------------------------------------
>
>
> Date: Sat, 17 Dec 2011 17:39:47 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] energy_terms
>
> On 17/12/2011 5:25 PM, balaji nagarajan wrote:
>
>     Dear Users !
>
>     I have used the energy group option to split the energy terms ,
>     for the protein and the water.
>
>
> You have split the *non-bonded* terms.
>
>
>     It gives all the terms ,
>
>     protein-protein , water-water , water-protein .
>
>     I have a doubt ,
>     the distance and the angle are taken for both water and the protein ,
>
>
> I don't see what distance and angle you mean.
>
>
>     how one can get these energy terms for protein alone.
>
>
> What energy terms do you want? You have the intra-protein non-bonded 
> energies above.
>
> Mark
>
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