[gmx-users] drug-enzyme simulation.

[Neha Gandhi]

Many thanks Justin,

It worked!

2009/3/29 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> Neha Gandhi wrote:
>>
>> Hi List,
>>
>> 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated
>> annealing followed by  production runs of 5ns usng NPT and PBC and
>> PME.. After 5ns, the protein moves far away from the ligand.  I
>> checked the 4ns gro files, the ligand and protein are bound together,
>> but its only that 5ns gives issues.
>>
>> 2) I ran another similar but smaller system and the complex is stable
>> even after 8ns.
>>
>> What went wrong with the simulations in case 1? Is there a way to fix
>> this problem?
>
> Did the protein and/or ligand cross a periodic boundary?  If so, trjconv can
> "fix" this visualization artifact.
>
> -Justin
>
>> Your help is much appreciated.
>>
>>
>> Regards,
>> Neha Gandhi,
>> School of Biomedical Sciences,
>> Curtin University of Technology,
>> GPO Box U1987 Perth,
>> Western Australia 6845
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> 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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-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845