[gmx-users] Problem with Umbrella Sampling simulation

[Justin Lemkul]

On 7/22/16 8:19 AM, Daniele Veclani wrote:
> Dear Gromacs Users
>
> I'm trying to calculate the potential mean force between two molecules (A
> and B).
>
> I created the various configurations through the pull simulation. To do
> this I kept fixes the position of the molecule A (position restraint)
>
> I have extracted the coordinates and sampled the various configurations.
>
> Now I have to use these configurations as input for umbrella sampling
> simulation.
>
> I have a couple of questions:
>
> - Do I have to maintain a position restraint on A molecule?
>

No.

> - Do I have to enter the position restraint even for molecule B? (Otherwise
> during the dynamic simulation I a change of the distance between molecule A
> and B)
>

No.  The distance between A and B is all that matters and it is restrained using 
the harmonic potential applied by the pull code.  It will vary over time but 
should on average, in each window, be equal to the restraint reference distance 
specified in the .mdp file.

-Justin

> - Can I get a clear explanation about this last step of the job?
>
> Best regards,
> D.V.
>

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

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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