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

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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