[gmx-users] pbc problems

Justin Lemkul jalemkul at vt.edu
Wed Mar 5 03:13:18 CET 2014

On 3/4/14, 8:35 PM, 申昊 wrote:
> Hello everyone!
> I am a new one of gromacs. When a simulation of protein in water is finished,
> should i first use the command of trjconv to remove pbc conditions(with
> nojump or mol), and then began analyze the new trajectory(rmsd, Rg and some
> other parameters)? Is the result believable without removing the pbc
> conditions or it is necessary for some specific calculations?

Most Gromacs programs deal with PBC with no manipulation required, some do not. 
  g_rms needs a properly processed trajectory.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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