[gmx-users] About periodic image of system.......

[Justin Lemkul]

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

-- 
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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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