[gmx-users] About periodic image of system.......
ramadavidgroup at gmail.com
Sat Nov 10 16:22:24 CET 2012
Thank you justin,
I actually check these file in vmd by seeing its periodic image , but
I not seen any problem in PBC.
As per you, If protein contain multiple chain, I have to make the index
group for each one.
Then I have to check each one by g_mindist -pi Is these right???
But what wiil be the problem if I used the whole group????
Still I not get the your explanation..Pardon me, but please explain it
On Sat, Nov 10, 2012 at 8:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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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