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

[rama david]

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
again??


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
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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