[gmx-users] virtual site in solvation free energy

Qin Qiao qiaoqin47 at gmail.com
Fri Dec 28 15:21:08 CET 2012

Dear all,

I want to get the solvation free energy of a molecule. The molecule itself
contains dummy atoms for virtual sites to fix its geometry. I used
'energygrp_excl' to exclude energy involved in virtual sites. However,
after I turned on the free energy parameters, the positions of the virtual
sites cannot be kept any more. Could you me some advice?

Thanks in advance.

mdp files for free energy part:

free-energy              = yes
couple-moltype           = 4dummy
init-lambda              = 0.1
; these 'soft-core' parameters make sure we never get overlapping
; charges as lambda goes to 0
sc-power                 = 1
sc-sigma                 = 0.3
sc-alpha                 = 1.0
; we still want the molecule to interact with itself at lambda=0
couple-intramol          = no
couple-lambda1           = vdwq
couple-lambda0           = none
foreign-lambda           = 0 0.1 0.3 0.5 0.7 0.8 0.9 1
nstdhdl                  = 100



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