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
trajectory.
-Justin
Kind regards
Thales
2014-06-17 8:56 GMT-03:00 Batdorj Batsaikhan <batsaikhan...@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
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