[gmx-users] how to set B-state locations for absolute position restraints while doing FEP computations

Christopher Neale chris.neale at alum.utoronto.ca
Tue Dec 10 00:20:40 CET 2013

Dear Users:

Does anybody know how to set the B-state values for position restraints?

I ask because I'm doing FEP of one part of the system, but I want to keep absolute position restraints on a different part of the system.

What I want to do is like this:

free-energy = yes
init-lambda = 0
couple-lambda1 = vdw
couple-lambda0 = none
couple-intramol = no
couple-moltype = LIGAND

It works fine without the position restraints. However, when I add the position restraints, the B-state values are set to zero's so I need to explicitly set it so that the B-state values for the location of the position restraints is the same as the A-state locations.

Here is a block of text from gmxdump that shows that my B-state positions for the position restraints are set to zero.

      posres_xA (3x3):
         posres_xA[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
         posres_xA[    1]={-4.20001e-02, -7.80001e-02, -3.50000e-02}
         posres_xA[    2]={-7.30001e-02,  6.19999e-02, -1.99997e-03}
      #posres_xB           = 0

This is fairly unexpected behaviour (note the force constant is not set to zero so the restrained atoms are all dragged to the Cartesian origin) and any help would be great.

Thank you,

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