[gmx-users] Center of mass removal for a trajectory which is already created
fpoosaneh at gmail.com
Fri Nov 13 13:39:40 CET 2015
Justin, thanks for comment.
In fact I am going to analyze g_density, but I see center of mass moves. I
have two-component system which has phase separated after a very long time.
I can't redo the simulation.
I could not mange that by tajconv.
Can I take the final .gro file of current simulation and run it with COM
removal to collect density?
On Fri, Nov 13, 2015 at 1:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 11/13/15 4:06 AM, Faezeh Pousaneh wrote:
>> Please some one help me how to remove center of mass motion in a
>> which is already created without this setting? is that possible?
> Not using COM motion removal during the run leads to artifacts; no amount
> of post-processing will fix that. If you're just looking to re-center some
> molecule(s) of interest, that's what trjconv is for.
> 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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