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
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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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