[gmx-users] Testing gromacs: Thermodynamics integration using tabulated potential
fahimeh.baftizadeh at gmail.com
Tue May 27 20:09:59 CEST 2014
Thanks for your reply.
Before this test, I have performed several thermodynamics integration playing with the number of lambda points and also decoupling first coulomb and then VDW or decoupling both at the same time. All my tests gave the same results as long as I am not using tabulated form of potential. In all of them, I obtained 74kj/mol as solvation free energy!
Now, my question is that, why using tabulated potential makes that much of a difference?
Do you mean that decoupling both Q and VDW can be a problem while using tabulated potential? In any case, I will lunch a simulation decoupling them separately and will update you.
I really appreciate your help
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.
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.
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
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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