[gmx-users] ligand-protein simulation

[Justin Lemkul]

On 11/1/13 5:37 AM, xiao wrote:
> Dear all gromacs users,
>
> I have run a protein-ligand simulations. However, the position of the ligand
> is not reasonable after 10ns simulation. There is no problem with the force
> field paramers of the ligand. I am trying to constrict the ligand move for
> 500ps simulation. But i do not know whether it will work. Any good idea is
> appreciated :)
>

Usually when something misbehaves, the topology is the first likely source of 
error.  How have you concluded that it is suitable?

Since we don't know what you're doing (description of your protocol, or even 
better, .mdp files), it could simply be that you're doing something that causes 
the physical model to be wrong.  Provide that information and you're more likely 
to get a quick and productive response.

-Justin

-- 
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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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