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

Fahimeh fahimeh.baftizadeh at googlemail.com
Tue May 27 19:53:39 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 files, 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 other parameters for VDW interactions are untouched. 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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