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

[Justin Lemkul]

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

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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