[gmx-users] About free enrgy calculation

[vidhya sankar]

Thank you for your previous reply 

Sorry  In previous Mail i wrongly  stated that decoupling CNT ( as you stated  it is big  Molecule ) 

To do free energy calculation based on on your tutorial 6( methane/water)   

I  want to decouple  Water  from CNT which is Wrapped by  assembly of Cyclic peptide  (the stability of assembly is mainly due to Vandewall's interaction between CNT and cyclic peptide)

When  I  Fix  following  parameter for My system    in mdp files
free_energy              = yes
init-lambda         = 0.00
delta_lambda             = 0.00
sc-alpha                 = 1
sc-power                 = 2.0
sc-sigma                 = 0.3 

It show follwin Notes How to Avoid this?

NOTE 1 [file /usr/local/gromacs4.6.11single/bin/MDP/em_steep_0.mdp]:
  With PME there is a minor soft core effect present at the cut-off,
  proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
  energy conservation, but usually other effects dominate. With a common
  sigma value of 0.34 nm the fraction of the particle-particle potential at
  the cut-off at lambda=0.5 is around 2.4e-04, while ewald-rtol is 1.0e-05.




May i extend your tutorial parameter  to my system ? because you also Decouple water from Metahne . Or is ther is Any Thump rule 



with regards
S.Vidhyasankar