On 18/12/2011 11:28 AM, Mark Abraham wrote:
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.
Of course, if you used a rigid water molecule for the simulation, then
there are already no bonded contributions from water.
Mark
Mark
thanks in advance
------------------------------------------------------------------------
Date: Sat, 17 Dec 2011 17:39:47 +1100
From: mark.abra...@anu.edu.au
To: gmx-users@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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