[gmx-users] Concerns with g_wham
jrcasey20 at gmail.com
Thu Apr 15 01:27:49 CEST 2010
I have been using g_wham, but I have a few questions that I can't find
answers to online. When using WHAM, one does not need the forces between
the pull groups to calculate the PMF, yet g_wham won't run without it. Is
there a reason for this?
Also, when using the pull code, I am allowed to define the spring constant K
for umbrella sampling, but I do not designate where the umbrella potential
is centered. How does gromacs determine this? I am interested as I would
like to create a PMF using umbrella integration (from code I will write
myself) rather than use WHAM. To do this and still use the umbrella
sampling runs used with GROMACS, I need to know where my umbrella potentials
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