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: [email protected]
To: [email protected]
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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