Hi,
we had similar trouble some time ago, and we could solve it by using a
good PBC atom. Make sure that your pbc_atom is in the very center of
your membrane.
Btw, using "distance" to compare with "cylinder" is a bad test, since it
does something very different (the distance is the same at z=com-1 and
z=com+1. I would use "direction" or "position" for your test. You can
also use position/direction for the umbrella simulations, you'll
probably get similar results to the geometry "cylinder", but you'll also
have to make sure your pbc_atom is fine.
Cheers,
Jochen
Am 4/29/12 9:20 PM, schrieb J B:
> Does the cylinder geometry work if you use "pull_start = no" and
pull_init1
> equal to your starting (restraint) distance? I'm just trying to go
through all
> of the iterations of what might be failing. In theory, what you're
doing is
> fine but I'd be interested to know if there was something failing in
the input
> parsing such that pull_start is not being properly applied. The
screen output
> of grompp will also tell you what it believes the restraint distance
is. If it
> prints 0, then there's a problem with input processing.
>
> If the problem is reproducible in the latest Gromacs version (4.5.5),
please
> file a bug report on redmine.gromacs.org so that it can be
investigated. Please
> provide .tpr file of the system so that the developers can run what
you are
> trying to do and see.
>
> -Justin
It works if I set pull_start to the initial distance given by g_dist
things work just fine.
So this will be the way for now at least.
Guess that there could be an error in the inout parsing then.
Thanks a lot for your help, really appreciate it.
--
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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