[gmx-users] Free Energy code

[Ali Khodayari]

Dear all,

 

I am quite new to free energy calculation, so I apologize if the questions
seem naive and of course they are a lot.

My intention is to turn off vdw and coulombic interactions to perform some
tempering cycles on my system. There are though some questions:

1-      I only want to decouple interaction in some part of my system, I
have put all the desired residues in groups in the index file. What should I
indicate for the couple_moltype line? As the system consists of large number
of atoms in the same molecule type. Introducing a new molecule type is not
possible because the atoms are connected chain-wise and I want to decouple
the interactions in the middle of the chain.

2-      Is it ok if I don't set the charges to zero from the beginning, and
proceed with turning them off step by step like what is done for the vdw in
the free energy tutorial?

3-      We are only interested in the end state where the interactions are
off. Can I decrease the number of spacings? Since we are not going to
measure the free energy, and we only intent to bring the system to an state
where the interactions are excluded for only part of the system.

4-      Since we are going to perform multiple tempering simulations,
maintaining the state B (non-bonded interactions off),  for each temperature
change, shall I keep indicating init_lambda_state = "last one, let's say 20"
and still maintain the last value of the λ array? So something like: 0.00
0.05  0.10  .  0.90  0.95  1.00  1.00  1.00  1.00  1.00  1.00  1.00?

Thank you for your responses, and sorry for the long email.

Kind regards,

Ali