[gmx-users] hydration free energy

dgfd dgdfg roinato at mail.ru
Fri Jan 5 15:09:15 CET 2018

>Do you know which values of lambdas are used?
>Are you using a soft-core technique?
Thanks for discussion. I am waiting already few days for anyfing reply. The technique of calculation in the file job.sh. The value of coul- λ is uniformely increasing from 0 to 1 with the step 0.02 for 50 first  λ- steps and in the same way for vdw- λ last 50  λ- steps. The problem is in the last trajectory with  λ=1 there are no coulomb and vdw intermolecular interactions with the estimate of the entropy according BAR method S=62204236256674537472.00 kT. The neigbouring state used in BAR with  λ=0.99 contains no coulomb and some remaining vdw force. Therefore I consider that overlapping of atoms can't produce this error. It happens only then opposite coulomb charges overcome vdw in nearly decoupled state. Therefore there is no need in soft-core interactions because all coulomb is decupling previously to vdw.
I made the search in archive and this problem was discussed sometimes, but didn't found clear answer for my case. Now I decided to run the cycle in the reversed order from decoupled state to real interactions.


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