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

Mark Abraham mark.j.abraham at gmail.com
Tue May 27 18:38:52 CEST 2014


Decoupling both q and vdw at the same time is not a good idea. You should
observe that at nearly-disappeared lambda, the error bars grow dramatically.


On Tue, May 27, 2014 at 5:38 PM, Fahimeh
<fahimeh.baftizadeh at googlemail.com>wrote:

> 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
> Fahimeh
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