[gmx-users] g_wham with cylinder geometry

MPID mpmcgovern at wisc.edu
Sat Feb 11 01:22:18 CET 2012

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.

More information about the gromacs.org_gmx-users mailing list