[gmx-users] solvation energy calculation
itamar.kass at gmail.com
Wed Nov 11 07:26:25 CET 2009
I am trying to repeat the solvation energy calculation as done by
Villa and MArk in (A. Villa and A. E. Mark Calculation of the free
energy of solvation for neutral analogues of amino acid side chains.
J. Comput. Chem, 23 (2002) 548-553.).
I am not sure about the way I am doing my in vacuum simulation.
attached is my mdp:
integrator = sd
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = berendsen
; Groups to couple separately, time constant (ps) and reference temperature (K)
tc-grps = system
tau-t = 0.1
ref-t = 298
; Pressure coupling
Pcoupl = no
; Generate velocites is on at 290K - do not get velocity from gro file.
gen_vel = yes
gen_temp = 290
ld_seed = 12
; Free energy control stuff
free-energy = yes
init-lambda = 0 ; Topology A (lambda=0) to topology B (lambda=1).
delta-lambda = 0
sc-alpha = 0.5 ; soft core potantial
sc-power = 1
sc-sigma = 0.3
; Center of mass control
nstcomm = 10000
; Periodic boundary conditions
pbc = xyz
comm_mode = angular
My question are:
1. Is there any meaning or temperature when one does SD in vacuum?
2. Does my lambda parameters ore fine?
3. Does the way I treat the center of mass motions is OK?
"In theory, there is no difference between theory and practice. But,
in practice, there is." - Jan L.A. van de Snepscheut
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at med.monash.edu.au
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