[gmx-users] Strange behaviour of bonds

[Justin A. Lemkul]

On 6/17/12 11:50 AM, Shima Arasteh wrote:
> OK, thanks.
> But may these lines in md.mdp file change the result and solve the problem?
>

There is no problem to be fixed.  Simply post-process your trajectory in a 
suitable manner (using the suggestions from the link I posted earlier).  The 
strange-looking bonds arise from "broken" molecules translating across the 
system.  This is a normal consequence of PBC.

> ; COM motion removal
> ; These options remove motion of the protein relative to the solvent/ions
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = Protein_Water
>

For a simple protein in water system, comm-grps should be set to "System." 
Hopefully you're not resetting COM motion of some parts of the system and not 
others.  In any case, this setting is irrelevant to the problem at hand.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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