[gmx-users] pbc problems

Justin Lemkul jalemkul at vt.edu
Wed Mar 5 12:08:06 CET 2014

On 3/5/14, 1:08 AM, 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
> Thank you for your response!
> As you said, i also found the Rmsd by using -nojump or -mol is different from that without these commands. And i can not
> decide which one is more accurate. Furthermore, can you list some other parameters that need removed pbc conditions?

RMSD will either be a normal-looking plot or something insane with massive 
changes when the molecule of interest jumps across a boundary.  The one that is 
"right" should be fairly clear under those circumstances :)

> such as SDF calculation ...

SDF needs a fitted reference, corrected for both PBC and translation/rotation. 
Exact instructions for such manipulations are given in the help text of g_spatial.



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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