[gmx-users] free energy questions

[MURAT CETINKAYA]

Hi,

I have a couple of questions about FE calculations. I am following the tutorial
by Dill group for calculating the solvation FE of a non-standard residue. 

1) Trivial questions first: It is advised to use PME with opls, is it possible
to use PME in vacuo? As far as I know PME depends on periodicity, which is
shut-off in vacuo.

2) Should I extract dv/dl values from my .edr file to get dG? Can I use dgdl.xvg
file? It is trivial but I am confused about this procedure.

3) I have smooth simulations when init_lambda < 1. But When I get to lambda =1,
I sometimes get enormously high energy values (in a fluctuating manner) for my
system. What could be the problem?

4) As you see in the mdp file, I used sc_alpha = 0. Otherwise, my system gives
out error. Is it bad to use sc_alpha =0?

5) Should I use FE parameters in my energy minimization simulations? Normally, I
used my minimized lambda=0 structure as input for other lambda simulations
without doing further EM. I also tried to include lambda values in my EM files
and I got junk results (.gro files and energy values).

and this is my mdp file for in vacuo MD:
title                    = MD in vacuo
cpp                      = /lib/cpp
include                  = -I/../EM/
integrator               = sd
tinit                    = 0
dt                       = 0.001
nsteps                   = 2500000
; number of steps for center of mass motion removal =
nstcomm                  = 100

nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 0
nstlog                   = 5000
nstenergy                = 5000
nstxtcout                = 0
xtc-precision            = 1000
;xtc_grps                 = Protein

nstlist                  = 10
ns_type                  = grid
;pbc                      = xyz
rlist                    = 1.4
coulombtype              = Shift
rcoulomb                 = 1.2
rcoulomb_switch          = 1.0
epsilon-r                = 1.0
vdw-type                 = Shift
rvdw                     = 1.2
rvdw_switch              = 1.0

DispCorr                  = EnerPres

;OPTIONS FOR TEMPERATURE COUPLING
tc_grps                  = system
tau_t                    = 1.0
ref_t                    = 300
;OPTIONS FOR PRESSURE COUPLING
Pcoupl                   = No
tau_p                    = 0.5
compressibility          = 4.5e-05
ref_p                    = 1.0 
; Free energy control stuff
free_energy              = yes
init_lambda              = 1.0
delta_lambda             = 0
sc_alpha                 =0.0
;sc-power                 =1.0
sc-sigma                 = 0.3 
; GENERATE VELOCITIES FOR STARTUP RUN = meaningful only with md integrator
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = -1

thanks in advance.

Murat CETINKAYA, M.Sc.
BioNanoMaterials Group,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176