[gmx-users] How to fix protein went out water?

Justin Lemkul jalemkul at vt.edu
Tue Jun 17 17:02:03 CEST 2014

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
> Thales
> 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,
>> Batsaikhan
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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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