[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
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list