[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

Dan Gil 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.

On Gromacs/4.6:
pull =umbrella
pull_geometry =distance
pull_dim =N N Y
pull_init1 =0
pull_k1 =100
pull_nstxout =100
pull_group0 =SOL
pull_group1 =a_Cooh

My attempt with Gromacs/5.1:
pull =yes
pull-ngroups        = 2
pull-ncoords        = 1
pull-group1-name = a_Cooh
pull-group2-name = SOL
pull-coord1-type  = umbrella
pull-coord1-geometry =distance
pull-coord1-groups     = 1 2
pull-coord1-dim =N N Y
pull-coord1-start        = yes
pull-coord1-init          =0
pull-coord1-k        =1000
pull-print-components = yes
pull_nstxout =100

Best Regards,


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