[gmx-users] Replica Exchange with Solute Tempering

[佐藤 千夏]

Dear Colleagues,
 
In order to conduct the replica exchange with
solute tempering,
I prepared two potential files, Va and Vb
[DOI:10.1002/jcc.21703],
then I want to do Hamiltonian replica
exchange next.
I saw the following page;
http://www.gromacs.org/@api/deki/files/177/=fe_tutorial.pdf
 
But, currently, I am not able to use the Vb
file, with the options,
 
free-energy             = yes
sc-power                = 1
sc-sigma                = 0.3
sc-alpha                = 1.0
couple-intramol         = no
couple-lambda1          = vdwq
couple-lambda0          = none
init-lambda-state       =
$LAMBDA$
fep-lambdas             = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
0.8 0.9 1.0
 
Is it correct to use these options?
How can I use both files describing the two
states A and B 
(when I couple to free energy
calculation with lambda parameter) ?
The version of GROMACS used is 4.6.6.
 
Thank you in advance.
best regards,
 
Chika