[gmx-users] Using polarizable ff for ions in conjunction with free energy calculation

Tom Kirchner tomkirch at mis.mpg.de
Sun Apr 15 10:23:49 CEST 2012

Hi all,

I'm working on MD simluations including Free energy calculations of 
polarizable water and polarizable ions. Normal MD simulations for water 
and ions are working fine. But when starting Free Energy calculation for 
ions+water, the simulation immediately aborts, giving the error:

/Program mdrun_d, VERSION 4.5.5
Source code file: [...]/src/gromacs-4.5.5/src/mdlib/shellfc.c, line: 365

Fatal error:
polarize can not be used with qA != qB/

Indeed, the ion force field consists only of the atom and the shell 
particle with different charges:

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge
1       ClA     1       ClI              ClA      1      2.630841e+00
2       ClS     1       ClI              ClS      1     -3.630841e+00

Even in the case, when init-lambda=0, which should be equal to a normal 
MD run, the error is obtained.

The lines to control Free Energy calculations are the following:

/free-energy        = yes
init-lambda        = 0.0
delta-lambda        = 0.00
foreign_lambda        = 0.167
sc-alpha        = 0.0        ; soft core is turned off for Coulomb 
sc-sigma        = 0.0
sc_power        = 1.0

couple-moltype        = solute    ; name of moleculetype to decouple
couple-lambda0        = vdw-q        ; all interactions are on at start
couple-lambda1        = vdw        ; turn off coulomb interaction
couple-intramol        = no
nstdhdl            = 100

separate_dhdl_file    = yes/

Free Energy calculation works for non-polarizable ff. If someone could 
help me, I would be very grateful.

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