[gmx-users] Analyzing Desmond trajectories using GROMACS tools
jalemkul at vt.edu
Mon Mar 6 16:26:42 CET 2017
On 3/6/17 10:16 AM, zeineb SI CHAIB wrote:
> Dear Justin,
> Thank you very much for your help and clarifications.
> I have a question please:
> I used OPLS-3 force field when running my simulations with Desmond, which is absent in GROMACS 5.1.3
> In order to generate the topology (protein and POPC), I guess I have to work with the same force field in GROMACS, OPLS-3.
> There is differences between OPLS3 and the OPLS that is implemented in GROMACS and I'm wondering if I can choose the latter when generating the topology and the rtp file for the analysis of my trajectories. May I have your opinion please?
None of the analysis methods you mentioned before will depend on the force field
parameters. Very few analysis routines do, anyway. The force field is critical
to determining the physical behavior during the simulation, not after it.
> Thank you in advance for your help.
> Best regards.
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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