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On 15/11/2011 10:21 AM, Sanku M wrote:
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<div>Hi,</div>
<div> I have a system containing water and a large protein. In
the simulation, I do not want the protein center of mass to
drift away.</div>
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<br>
Why do you want it not to drift away? There's nothing magical about
the center of a periodic simulation cell. Why do you want to change
the dynamics to achieve this?<br>
<br>
Mark<br>
<br>
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new roman, new york, times, serif;font-size:12pt">
<div> I was wondering what will be the reasonable method in
gromacs to fix the position of the center of mass of the
protein in its original position . I was thinking about two
options in gromacs.</div>
<div> 1) use the protein as comm-grp only to remove its center
of mass motion . ( or should I use both protein and
non-protein ( water) center of mass as comm-grps separately ).</div>
<div> 2) Finding the residue closest to center of mass of the
protein ( but I am not sure how to do it ).</div>
<div>Can anyone suggest which will be a good idea ?</div>
<br>
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<br>
<br>
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