Dear Gromacs experts,
I'm just a newbaby in Gromacs, and hence I have a lot of problem
when running this program. I try to run NVE simulation of a
protein. First, I run an NTP ensemble, follow by NVT and finally,
NVE. In NPT and NVT, T remains as constant, however, in NVE
simulation, the temperature drops gradually instead of maintain
approximately constant. Could you give me any advice to solve this
problem?
Thank you very much.
Regards,
Nguyen
P.S: below is my mdp file for three simulations:
NPT ensemble:
title = DEN2pro_MD
define = -DFLEXIBLE
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 2000 ps.
nstcomm = 1
nstxout = 5000 ; output coordinates every 10 ps
nstvout = 5000 ; output velocities every 10 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc_grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
NVT ensemble
title = DEN2pro_MD NVT equilibration
define = -DPOSRES ; position restrain the protein and ligand
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 100000 ; 2 * 100000 = 200 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 5000 ; save coordinates every 10 ps
nstvout = 5000 ; save velocities every 10 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
energygrps = Protein
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 0.9 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature,
one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
NVE ensemble:
title = DEN2pro_MD NVE equilibration
define = -DPOSRES ; position restrain the protein and ligand
; Run parameters
integrator = md-vv ; leap-frog integrator
nsteps = 1000000 ; 2 * 1000000 = 2000 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 5000 ; save coordinates every 10 ps
nstvout = 5000 ; save velocities every 10 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
energygrps = Protein
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.6 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
rlistlong = 1.6
;treatment of van der waals interactions
vdwtype = Shift
rvdw = 0.95 ; short-range van der Waals cutoff (in nm)
rvdw-switch = 0.9
; Electrostatics
coulombtype = PME-Switch; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = no ; no temperature coupling in NVE
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVE
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
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