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On 18/12/2011 11:28 AM, Mark Abraham wrote:
<blockquote cite="mid:4EED33AE.4040003@anu.edu.au" type="cite">
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On 18/12/2011 3:56 AM, balaji nagarajan wrote:
<blockquote cite="mid:SNT123-W457FA44E772B7EF410601FE2A10@phx.gbl"
type="cite">
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<div dir="ltr"> <br>
Dear Users ! <br>
<br>
I can print the values of the bonded and non bonded energy
terms of the protein and the water , <br>
<br>
I have used the group option , <br>
<br>
I want to know the bonded contribution only from the protein ,
<br>
in case of the torsion energy term it is only for the protein
, <br>
<br>
The bond distance and the bond angle , the contribution from
the water is also there , so how one can get these <br>
terms for protein alone . <br>
</div>
</blockquote>
<br>
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.<br>
</blockquote>
<br>
Of course, if you used a rigid water molecule for the simulation,
then there are already no bonded contributions from water.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:4EED33AE.4040003@anu.edu.au" type="cite"> <br>
Mark<br>
<br>
<blockquote cite="mid:SNT123-W457FA44E772B7EF410601FE2A10@phx.gbl"
type="cite">
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thanks in advance <br>
<br>
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<br>
Date: Sat, 17 Dec 2011 17:39:47 +1100<br>
From: <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>
To: <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: Re: [gmx-users] energy_terms<br>
<br>
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On 17/12/2011 5:25 PM, balaji nagarajan wrote:
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cite="mid:SNT123-W340E99AE5A1F71C1B8AE23E2A10@phx.gbl">
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<div dir="ltr"> Dear Users ! <br>
<br>
I have used the energy group option to split the energy
terms , for the protein and the water. <br>
</div>
</blockquote>
<br>
You have split the *non-bonded* terms.<br>
<br>
<blockquote
cite="mid:SNT123-W340E99AE5A1F71C1B8AE23E2A10@phx.gbl">
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It gives all the terms , <br>
<br>
protein-protein , water-water , water-protein .<br>
<br>
I have a doubt , <br>
the distance and the angle are taken for both water and
the protein , <br>
</div>
</blockquote>
<br>
I don't see what distance and angle you mean.<br>
<br>
<blockquote
cite="mid:SNT123-W340E99AE5A1F71C1B8AE23E2A10@phx.gbl">
<div dir="ltr"><br>
how one can get these energy terms for protein alone.<br>
</div>
</blockquote>
<br>
What energy terms do you want? You have the intra-protein
non-bonded energies above.<br>
<br>
Mark<br>
<br>
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