lammps-users Digest, Vol 134, Issue 83

From: Lamm Gro <lammgro@…24…>

Subject: [lammps-users] Free energy

Date: 26 July 2017 at 07:16:46 GMT+1

To: lammps-users <[email protected]>

Dear Lammps users ,

I try to calculate the free energy of water with FEP method .
( free energy of one water molecule inside of a box of it ) .
Unfortunately I just get 0.0 amount for free energy !
Can you please let me know what might be problem ?

Does your installation reproduce the tests/examples?
If so, maybe you should proceed in small modifications from there until you fully understand the commands.

I am not going to check your input file line by line. However, some things look strange.

  • As I see types 3 4 is the “solute” and 1 2 is the “solvent”. So why do you use soft potentials for solvent-solvent interactions?
  • I J pairs should by given as I <= J
  • you should adapt the lambdas on Hw-* interactions too because it affects the real space part of Coulomb.
  • the delta in activation parameter lambda seems very small and the number of timesteps at each stage very large. It should be possible to have a good value of free energy with less effort (my guess).

Maybe there are more issues.

As I wrote to you a few times before, this does not seem to be the good method to learn.

Agilio

Dear Prof.Padua .

Thanks for your reply , I really appreciate that .
In parallel with this simulation i also study this book : Free Energy Calculations . Theory and Applications in Chemistry and Biology
and this paper : J. Am. Chem. SOC., Vol. 110, No. 18, 1988 .

Best Regards,
Saeed.