Hi Justin, Thank you very much for your response. I used GAFF force field parameters for the ligand. I have done another short MD simulation, and this time everything seems fine, so i have no idea where the problem is from. Best wishes Fugui
At 2013-11-01 20:41:46,"Justin Lemkul" <jalem...@vt.edu> wrote: > > >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 > >-- >================================================== > >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 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >================================================== >-- >gmx-users mailing list gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >* Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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