[gmx-users] Com pulling in reverse Z direction in SMD simulation..

[Kalyanashis]

Thank you Justin. I got the point. Whatever you have replied those were my
query. Actually I could not able to push the drug molecule to the active
site and md run was finished normally without any error. Thank you once
again Justin....


On Thu, Apr 24, 2014 at 8:35 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5016046h13 at n6.nabble.com> wrote:

>
>
> On 4/24/14, 10:46 AM, Kalyanashis wrote:
> > Thank you Justin.. I have done the calculation with "pull_vec1= 0.0 0.0
> 1 "
> > option but do not get the expected result. Actually, I want to push the
> > drug molecule to its initial position i.e. after pulling it has come out
> > from the active site of the enzyme now I want to push it to the active
> > site. Please suggest me the probable solution to solve this problem.
>
> I can't do that unless you describe what's going on in more detail.  What
> does
> "do not get the expected result" mean?  What happens?  Applying a pulling
> force
> in two different directions is very trivial; all you have to do is either
> (1)
> invert the sign of the vector or (2) invert the sign of the pull rate
> along the
> original vector.
>
> Trying to "push" a molecule towards an active site is a dicey proposition;
> the
> target can rotate over time and you may not be able to achieve the desired
> result without other restraints.  You're trying to hit a moving target.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
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-- 
Kalyanashis Jana
email: kalyan.chem.in at gmail.com


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