[gmx-users] Ions drifting

[Justin Lemkul]

On 12/16/14 1:34 AM, jani vinod wrote:
> Dear All,
> I am trying to carry out simulation of protein at 0.5 mM concentration of
> NaCl.
> It has been observed that within few nanosecond ions begin to drift in one
> direction and protein in other direction. I am using Amberff03 force filed.
> What may the reason for the same.
>

No idea unless you show us your .mdp file and any commands you're giving.  Is 
this drift observed in the raw trajectory, or in something you've manipulated 
with trjconv?

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================