NG HUI WEN wrote:
Hi all,
I have something here which I am would like to pick your brains. Thank
you in advance. In my trial-and-error attempt to equilibrate my membrane
protein system, I encountered this problem.
I was playing with 2 different mdp files (in succession), first by using
the Nose Hoover then v-rescale. I realised upon changing from the former
to the latter there was a drop in simulation temperature from 310K to
about 263K. Not sure if this have anything to do with the switch of
thermostat or due to some other parameter change?
The mdp file below which contain the Nose Hoover thermostat was used to
generate A3_1posre (see below grompp command)
title = NPT
define = -DPOSRES
; Run parameters
integrator = md
nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)
dt = 0.002
; Output control
nstxout = 50000
nstvout = 50000
nstenergy = 500
nstlog = 500
; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
; Temperature coupling is on
tcoupl = Nose-Hoover
tc-grps = Protein POPC SOL_CL-
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
ref_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
; Periodic boundary conditions
pbc = xyz
; Dispersion correction
DispCorr = EnerPres
; Velocity generation
gen_vel = no
; COM motion removal
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_POPC SOL_CL-
; Energy groups
energygrps = Protein POPC SOL_CL-
I then use another mdp file containing v-rescale thermostat to extend
the simulation
grompp –f v-rescale.mdp –c A3_1posre.gro –o A3_noposre.tpr -n
index.ndx -p topol_3.top
mdrun_mpi -s A3_noposre.tpr -v -cpi A3_1posre.cpt
The problem is likely here. You're switching the conditions of the ensemble
during mdrun. Normally, you would supply the .cpt file to grompp -t to preserve
all the state variables. In conjunction with "gen_vel = no" in the .mdp file,
the continuation is exact. Since you're not generating velocities with grompp
AND not supplying a .cpt file, the initial state will be hard to predict, but
likely will not correspond to the proper ensemble.
-Justin
title = NPT
define =
; Run parameters
integrator = md
nsteps = 1000000 ; 2 * 1000000 = 2000 ps (2 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 250000
nstvout = 250000
nstenergy = 1000
nstlog = 500
nstxtcout = 250000
; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
; Neighborsearching
ns_type = grid
nstlist = 10
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.12
; Temperature coupling is on
tcoupl = v-rescale
fluctuation
tc-grps = Protein POPC SOL_CL-
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 1.0
ref_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres
; Velocity generation
gen_vel = no
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_POPC SOL_CL-
; Energy groups
energygrps = Protein POPC SOL_CL-
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>>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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