[gmx-users] questions in Running MDS over docked poses

[vivek sharma]

hi Justin,
Thanks for your reply...
I am interested in looking for the stability of the docked pose, by applying
some temperature variation in the molecule.
If I am applying temperature variation then should I use pressure coupling
simultaneously.
Can you suggest some tutorial for such attempts.....

With Thanks,
Vivek

2008/11/10 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> vivek sharma wrote:
>
>> Hi There,
>> I am running MDS over the docked poses to check the stability of the
>> docked poses using gromacs.
>> I have few doubts about selecting parameters for the same, If anybody have
>> tried such thing earlier, please suggest me for the same.
>>
>> Should I keep pressure coupling over the simulation ?
>>
>
> Sure; life exists at NPT, so it is commonly used in routine protein
> simulations.
>
>  For how long should I run the simulation for such purpose ?
>>
>>
> That's up to you :)  You should run the simulations as long as you feel
> necessary to achieve stability.  I know that's vague, but there really is no
> single correct answer to this question in the MD field.  If there is, I'd
> love for someone to tell me, too...;)
>
> -Justin
>
>  Waiting for suggestions.
>>
>> With Thanks,
>> Vivek
>>
>>
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>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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