[gmx-users] Concerns with g_wham

Jennifer Casey 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
are centered.

Thank you,
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