[gmx-users] ligand moving out during umbrella sampling

Justin Lemkul jalemkul at vt.edu
Fri May 19 13:48:25 CEST 2017

On 5/19/17 5:56 AM, abhisek Mondal wrote:
> On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>>> This time I think I got ligand restrained successfully during the umbrella
>>> sampling. I have removed the restrain from protein, as per your advice.
>>> Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
>>> pull_rate1=0.0.
>>> I have uploaded the trajectory movie (and other mdp files) in the
>>> following
>>> link:
>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>> However, I'm facing a problem. Due to the withdrawal of the position
>>> restrain of protein. The protein and ligand (together) is moving around
>>> the
>>> box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
>>> than 0.49 times the box size (10.646989)" error.
>>> As per the video I have uploaded, if I assume this approach worked, then
>>> how can I avoid this error ? Is  there any way to make sure the
>>> protein-ligand remains in the middle of the box (or nearby). I have taken
>>> pretty large box compared to the protein structure from the beginning.
>>> Please suggest me a way out.
>> Use a larger box or use direction-periodic geometry.
>  For the sake of computational power I'm leaning towards direction-periodic
> geometry. However, from the mailing list entries I found out that pressure
> coupling should not be used for this kind of geometry setup.
> NVT coupling with no velocity generation is what I'm opting for. There are
> a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
> Would you please suggest if the code (
> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0) looks
> sensible ?
> Eagerly waiting for your opinion.

Try it and see what happens.



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


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