[gmx-users] Using COM pulling and Enforced Rotations together

Carsten Kutzner ckutzne at gwdg.de
Tue Jan 6 11:27:59 CET 2015

Hi Abhishek Acharya,

On 06 Jan 2015, at 11:06, Abhi Acharya <abhi117acharya at gmail.com> wrote:

> Hello Gromacs users,
> I would like to use COM pulling and Enforced rotations simultaneously on a
> single domain. Is it possible at all to do so?
Yes, absolutely!

> I tried to run an
> simulation; it ran fine without errors, but analysis indicates COM pulling
> may not have worked properly although the domain was rotated by the correct
> angle. I used the following parameters.
It does not work with all rotation potentials, only with
the pivot-free and the translation-invariant ones. Here,
the position of the rotational reference group is relative to
the COM of the rotation group, in the other cases, it is
fixed in space.

> ; Enforced rotation: No or Yes
> rotation                 = Yes
> ; Rotation group name
> rot_group0               = GD-C-alpha
> ; Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2,
> rm2-pf, flex, flex-t, flex2, flex2-t
> rot_type0                = flex
Use flex-t instead, this should do the trick.

What works with pulling: iso-pf, pm-pf, rm-pf, rm2-pf, flex-t, flex2-t

Happy pulling!

Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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