[gmx-users] How to fix protein went out water?
batsaikhanbat at yahoo.com
Wed Jun 18 07:34:04 CEST 2014
Thank you Justin and Thales.
On Tuesday, June 17, 2014 11:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
On 6/17/14, 10:54 AM, Thales Kronenberger wrote:
> Hi Batsaikhan
> You should re-do the simulation, perfoming it within a box of water with
> PBC (you can do this with the editconf)
There is no need to re-do anything. PBC means it is totally irrelevant whether
the protein is conveniently centered in the box or not; the forces are the same.
The protein drifting "outside" the box is a total non-issue, since there is no
such thing as "outside" of a periodic system. All one needs to do is apply
trjconv for convenient visualization, and no action needs to be taken to
continue the run; mdrun doesn't care about our conventions for watching the
> Kind regards
> 2014-06-17 8:56 GMT-03:00 Batdorj Batsaikhan <batsaikhanbat at yahoo.com>:
>> Dear gmx_users,
>> I am working on simulation of protein in water. 10 ns after the protein
>> went out from water. How to fix this? Can I continue my simulation?
>> Best regards,
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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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