[gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 11/9/13 9:38 AM, shahab shariati wrote:
> Dear Justin
>
> Thanks for your explanation.
>
> My system contains lipid bilayer + drug + water molecules.
>
> I want to calculate Potential of mean force as a function of the distance
> between the centers of mass of drug and the lipid bilayer.
>
> Box vector along which the pulling is being conducted is Z.
>
> 1) Are these issues true about my system?
>
> lipid bilayer = reference group for pulling.
> drug molecule = group to which pulling force is applied.
>
> Then, should I use position restraining on the lipid bilayer?
>

I see no reason for that.  The use of position restraints represents a special 
case, the logic for which is described in our paper.  Please do not extrapolate 
too literally from my tutorial to your system.

> 2) The system you considered was the dissociation of a single peptide from
> the growing end of an protofibril.
>
> So, in your summary_distances.dat, distance between chain A and chain B was
> increased.
>
> But, I want to consider translocation of the drug molecule from water into
> the lipid bilayer. On the other hand, I want to consider approaching drug
> molecule to lipid bilayer.
>
> So, in my summary_distances.dat, distance between drug molecule and lipid
> bilayer will be decrease.
>

...and then increase, if you want to study the partitioning across the membrane.

> My mean is that my case is contrary to your case. Nonetheless, should I use
> exactly Pull code section of your md_pull.mdp file?
>

Absolutely not!  Please refer to the advanced section of the tutorial.  The 
settings you will need will be very different from the tutorial, which 
represents the simplest possible case of pulling.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
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

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