[gmx-users] Drug moves out of the nanocarrier

[Justin Lemkul]

On 4/22/17 1:47 PM, faride badalkhani wrote:
> Dear Gromacs users,
> I am trying to perform PMF calculations on a nanocarrier-drug system. The
> procedure I have performed is as follows:
> 1) running MD simulation on the unloaded nanocarriers for 30 ns
> 2) insertion of drug into nanostructure using AutoDock
> 3) running production MD simulation on the nanocarrier-drug for more 30 ns
> 4) umbrella sampling and PMF calculations
>
> I have completed this procedure for 5 systems, but for the last one drug
> moves out of the nanocarrier after 5 ns, and I do not know how to sole the
> problem.
>

Either the docked pose is not stable or the drug topology is of poor quality.

-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 629
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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