[gmx-users] pbc problem

Justin Lemkul jalemkul at vt.edu
Wed Jan 29 14:20:53 CET 2014

On 1/29/14, 5:44 AM, Atila Petrosian wrote:
> Dear kannan
> Thanks for your reply
> Are you sure there is not pbc problem in my case.
> For example, can I do g_dist tool to obtain distance between protein and
> cnt? Is output for g_dist true and rational?

g_dist, like most Gromacs tools, accounts for periodicity, even without "fixing" 
the trajectory.  You can process the original and modified trajectories to see 
if they return the same result.  If not, you can easily visualize the modified 
trajectory to verify that it is re-imaged properly.



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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