[gmx-users] gibbs+umbrella+constraint

[parto haghighi]

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?