[gmx-users] g_wham with cylinder geometry

[Jochen Hub]

Hi MPID,

I just stepped over your message quite late, so sorry for the late reply.

You can simply generate a new set of tpr files with pull_dim= N N Y, and 
use that one in g_wham. g_wham only picks the force constants and 
umbrella centers from the tpr files, so you are fine with that.

Jochen


Am 2/11/12 1:22 AM, schrieb MPID:
> Hi everyone. I ran an umbrella sampling simulation of a protein in a
> membrane. I used pull_geometry=cylinder. I tried to analyze the results with
> g_wham. I got this error:
>
>   Fatal error:
> With pull geometry 'cylinder', expected pulling in Z direction only.
> However, found dimensions [Y Y Y]
>
> The manual says that with this geometry the pulling is in the direction of
> pull_vec. I set pull_vec to 0 0 1. Do I have to redo these simulations with
> a line that says pull_dim = N N Y? Or does the data still mean what it is
> supposed to, but g_wham is just giving trouble and I can use a different
> wham program?
>
> Here is the pull part of my mdp file:
>
> pull                     = umbrella
> pull_geometry            = cylinder
> pull_r0                  = 2.0
> pull_r1                  = 1.5
> pull_vec1                = 0 0 1
> pull_start               = yes
> pull_group0              = DPPGB
> pull_group1              = PROT
> pull_k1                  = 500
> pull_nstxout             = 1000
> pull_nstfout             = 1000
>
>
> --
> View this message in context: http://gromacs-users-forum.5086.n6.nabble.com/g-wham-with-cylinder-geometry-tp4385053p4385053.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

-- 
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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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