[gmx-users] gibbs+umbrella+constraint
parto haghighi
parto.haghighi at gmail.com
Sun Feb 12 12:28:17 CET 2012
Dear gmx users
I am working on an umbrella sampling system.(lipid bilayer+drug).
I have used distance
here is my mdp file for pulling:
title = Umbrella pulling simulation
define = -DPOSRES_LIP
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 2500000 ; 5 ns
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc_grps = DRG_DMPC SOL
tau_t = 0.5 0.5
ref_t = 310 310
; Pressure coupling is on
Pcoupl = Berendsen
pcoupltype = semiisotropic
tau_p = 5.0 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = LIPID
pull_group1 = DRUG
;pull_init1 = 0
pull_rate1 = -0.1
pull_k1 = 500 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
and also this is my umbrella mdp file:
title = Umbrella pulling simulation
define = -DPOSRES_LIP
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 500000 ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = DRG_DMPC SOL
tau_t = 0.5 0.5
ref_t = 310 310
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = LIPID
pull_group1 = DRUG
pull_init1 = 0
pull_rate1 = 0.0
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
I have used lipid as a refrence group and drug as a pull group.in
npt_umbrella mdp I have used constraint for refrence group and in
md_umbrella I have removed the constraint.
After that my summery.dat file contains following data:
0 2.2163574
1 2.2125353
2 2.1688467
3 2.1041310
4 2.0907198
5 2.0372755
6 2.0344109
7 2.0205807
8 2.0188276
9 2.0063477
10 2.0100271
.
.
495 1.6062210
496 1.5399962
497 1.5931936
498 1.6058899
499 1.6357416
500 1.5546903
I have applied 0,3,9,15,16,17,18,19,20,22,39,42 and 51 (from 0 to
500) points for my umbrella sampling.
My questions:
1.why do I have only two peaks in my histogram curve?
2.I have seen in a paper using constraint for pull,to calculate delta
G of system.I want to calcuate delta G of drug,what should I do?Any
diffrence in using umbrella or constraint?
3.What is the best way in our system to calculate delta G?
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