[gmx-users] About periodic image of system.......
jalemkul at vt.edu
Sat Nov 10 16:04:46 CET 2012
On 11/10/12 10:02 AM, rama david wrote:
> Dear justin,
> Thank you for your reply and explanation,
> My ligand is protein( 4 amino acid peptide).
> The group in index file PROTEIN contain both ligand
> and protein.
> The box size is 11.4942 10.7884 10.7884 at the time 16162 (ps).
> The box size I given in editconf is 11.40000 10.70000 10.70000
> So please would you told me the reason for my g_mindist value less than vdw
> cut off 1.4 ?????
Look at what those atoms are at that particular time point. The confusion
likely arises from the fact that you're selecting "Protein," which actually
contains multiple molecules, rather than a single protein molecule. Atoms can
come pretty close during a simulation, especially if they are involved in, for
instance, hydrogen bonds.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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