[gmx-users] hydration free energy

[asaffarhi at post.tau.ac.il]

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.


---------------------------

You're welcome.

If there are no vdW and Coul it still calculates the average energy,  
which without soft-core technique can be very large when atoms overlap.
You can read
http://www.sciencedirect.com/science/article/pii/S0010465516303411

Eq. (2) and the following text etc.

You can try a soft-core technique to see if it is better.

Best,
Asaf
Quoting dgfd dgdfg <roinato at mail.ru>:

> Hi,
>>
>> Do you know which values of lambdas are used?
>> Are you using a soft-core technique?
>>
>> Asaf
> 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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