[gmx-users] problem in binding free energy calculation and setting Lambda

[meisam valizadeh kiamahalleh]

Dear GMX Users

I would like to let you know that I have run MD simulation on a Carbon
nanotube- drug system.

All steps (Energy minimization, Postion restrained, Equilibration with NVT
and NPT ensembles and finally MD) have been done successfully. Currently if
would like to calculate binding free energy for the system (drug molecules
inside Carbon nanotube). Here are my questions at this point;

1.May I know if I must add the free energy stuff to all the mdp files for
each steps of (Energy minimization, Position restrained, Equilibration with
NVT and NPT ensembles and finally MD) and redo all the simulation steps? I
am wondering because I have seen few people who only edited the final MD.mdp
file and add the free energy stuff.


2. I know to get the binding energy curve; I need to run several
simulations, one for each lambda value.  Hence, I need 21 point from
Lambda=0 to 1 to get the smooth curve. To do this, I have to start with
initial Lambda =0 as stated in the energy stuff below, in my mdp file.  May
I know which parameter(s) (init_lambda or foreign lambda or ...) need to be
changed in my mdp file to do the next simulation and until the last
simulation? I mean to go from Lambda=0.0 to the next lambda =0.05, 0.10,
0.15, … and 1.00.

The free energy stuff in my mdp file is as below:


; Free energy control stuff

free_energy              = yes

init_lambda              = 0.00

delta_lambda             = 0

foreign_lambda           = 0.05

sc-alpha                 = 0.5

sc-power                 = 1.0

sc-sigma                 = 0.3


Your kind advice on this matter would be highly appreciated.

Best regards

Meisam
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