[gmx-users] Binding of a drug to a lipid bilayer using umbrella sampling method

[Justin Lemkul]

On 3/28/16 9:02 PM, Khuong Truong Gia wrote:
> Dear all,
>
> I am running umbrella sampling simulation about binding of a drug (polymer)
> to a lipid bilayer. Could you please suggest me how can I do
> position-restraints the reference group (bilayer)? Do I need to restraint
> all lipid molecules?

You should not have to apply position restraints to anything.

> As I read in the gromacs manual there is cylinder option for the
> pull-geometry, but I am not sure this is suitable for my system or not?
> Please give me some advice.

Yes, that is a good choice, as the example in the manual is almost identical to 
what you're doing.

-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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