[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling
dgilgmx at gmail.com
Sat Aug 6 19:34:47 CEST 2016
I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp
file that I am confused with.
I am pulling an atom of solute, indexed a_Cooh, towards the COM of solvent.
This is a slab geometry, with the plane normal to the z-axis direction. My
output (pullx.xvg) should contain the deltaZ value between the solute Z
coordinate and solvent COM z coordinate. With my current Gromacs/5.1
attempt, I don't think I am getting the correct results.
pull_dim =N N Y
My attempt with Gromacs/5.1:
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = a_Cooh
pull-group2-name = SOL
pull-coord1-type = umbrella
pull-coord1-groups = 1 2
pull-coord1-dim =N N Y
pull-coord1-start = yes
pull-print-components = yes
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