Den 2020-03-29 kl. 05:24, skrev Alex:
Dear all,
In a system, I have a thin_film (infinitive in x-y directions) with water
on top and bottom of it, PBC = xyz.
By the below flags I try to remove the motion of the center of mass of the
two group separately.
comm-grps = thin_film Water
comm-mode = Linear
nstcomm = 100
However the thin film drift specially in x and y directions whereas I was
expecting to have no drifting for the thin film, If I understood correctly
the usage of the comm-grps!
Would you please let me know how I can stop drifting of the thin film?
Thank you,
Alex
Is that a liquid film? Are there interactions within the film and with
water? The comm removal will calculate the center of mass taking
periodic boundaries into account so if your film moves one molecule at a
time the COM will stay in place. In a realistic system the friction
between water and film should prevent this, hav eyou tried turning off comm?
Historically this has been a fix for the Berendsen thermostat that
accumulates energy, however with a stochastic thermostat it should not
be necessary. Not sure about Nose-Hoover though.
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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