[gmx-users] UMBRELLA SAMPLING

[Justin Lemkul]

On 3/4/17 9:24 AM, Subashini .K wrote:
> Hi gromacs users,
>
>
> I want to calculate delta G for protein ligand binding.
>
>
> Had run the umbrella pulling simulation   for 100 ps (protein ligand solvated in water), applying restraint in the protein (using the code in gromacs tutorial website, Bevenlab).
>
>
> But, after running the perl script  (perl distances.pl), did not obtain any distance on the right column (summary_distances.dat). It was blank.
>
>
>
> (1) Had applied the position restrain of the protein during NPT equilibration.
>
> (2) During puling simulation, again applied the restrain on the protein. Is it correct?
>
>
> How to rectify the mistake and proceed in the right direction?
>

The script from the tutorial is designed for use with the tutorial and therefore 
makes assumptions about the groups that are in the index file.  Invoke gmx 
distance yourself so you can see how to properly use it, then adjust the script 
as needed.

-Justin

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

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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