[gmx-users] Testing gromacs: Thermodynamic integration using tabulated potential

Fahimeh Baftizadeh fahimeh.baftizadeh at googlemail.com
Tue May 27 00:27:33 CEST 2014

Hi everyone,

I am computing solvation free energy of molecule A in solvent B. I used two
different procedure and I thought that the results should be comparable,
however they are very different.

Procedure 1:
Thermodynamics integration using 20 lambda points. VDWtype was switch and I
used PME coulombtype.  I turned off VDW and coulomb interactions both at
the same time. The free energy of solvation was  74kj/mol

Procedure 2:
Thermodynamics integration using 20 lambda points. I introduce tabulated
potential for the interaction between molecule A and molecule B. therefore
the vdwtype and columbtype was set to User. I provided two file, called
table.xvg and table_A_B.xvg which are identical for now as a test. These
files contain, r, 1/r, 1/r**2, -1/r**6, -6/r**7, 1/r**12, 12/r**13. The
result of this simulation however is very different ~50kj/mol ...

I am expecting to receive not identical but something comparable ... could
you please help me to understand this?

Many thanks in advance

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