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Hello
i have one issue
the density is of my system during npt is nearly 1000kg/m3 , but for md production in npt ensemble
it is showing less then 1000kg/m3
i will share my npt.mdp as well as md production. mdp
; VARIOUS PREPROCESSING OPTIONS
title = NPT simulation (constant number, pressure and temperature)
cpp = /usr/bin/cpp
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.002
nsteps = 1000000
; OUTPUT CONTROL OPTIONS
nstxout = 2500
nstvout = 2500
nstfout = 0
nstlog = 2500
nstenergy = 2500
nstxtcout = 2500
xtc_precision = 1000
xtc-grps = System
energygrps = system
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = pme
pme_order = 4
fourierspacing = 0.16
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
ewald_rtol = 0.00001
; Temperature coupling
Tcoupl = v-rescale
tc-grps = system
tau_t = 1.0
ref_t = 300
; Pressure coupling
Pcoupl = Berendsen
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
DispCorr = EnerPres
refcoord_scaling = com
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no ; Assign velocities to particles by taking them randomly from a Maxwell distribution
gen_temp = 300 ; Temperature to generate corresponding Maxwell distribution
gen_seed = 135962 ; Seed for (semi) random number generation.
; OPTIONS FOR BONDS
constraints = all-bonds
constraint-algorithm = lincs
continuation = yes
shake-tol = 0.0001
; VARIOUS PREPROCESSING OPTIONS
title = Production Simulation
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0 ; Starting time
dt = 0.002 ; 2 femtosecond time step for integration
nsteps = 5000000 ; 10 ns
; OUTPUT CONTROL OPTIONS
nstxout = 100000 ; Writing full precision coordinates d
nstvout = 100000 ; Writing velocities d
nstfout = 0 ; Not writing forces
nstlog = 50000 ; Writing to the log file
nstenergy = 1000 ; Writing out energy information
nstxtcout = 1000 ; Writing coordinates
xtc_precision = 1000
xtc-grps = system
energygrps = system
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = pme
pme_order = 4
fourierspacing = 0.16
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
ewald_rtol = 0.00001
; Temperature coupling
Tcoupl = v-rescale
tc-grps = system
tau_t = 1.0
ref_t = 300
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = Isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
DispCorr = EnerPres
refcoord_scaling = com
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen_temp = 300
gen_seed = 314629
; OPTIONS FOR BONDS
constraints = all-bonds
constraint-algorithm = lincs
continuation = yes
shake-tol = 0.0001
; Input file
;
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 10000
;
nstxout = 2500
nstvout = 2500
nstfout = 0
nstlog = 2500
nstenergy = 2500
; Energy minimizing stuff
;
emtol = 10
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
pbc = xyz
please resolve the problem