[gmx-users] Effect of time step size
Faezeh Pousaneh
fpoosaneh at gmail.com
Tue Feb 10 12:17:04 CET 2015
Hi,
I am simulating methanol (using its topology given in Gromacs homepage, for
1728 molecules). I run the simulation (npt, P=1atm and T=290) for different
time step size, dt=0.001, 0.003 fs. But I obtain different results for each
of them:
783 kg/m^3 for dt=0.001
790 kg/m^3 for dt=0.003
Why is it so?
I have also checked the point for lutidine molecule and I see similar
behavior. Below is my production.mdb file:
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.001 ; 2 fs
nsteps = 30000000 ; 0.002 * 50000 = 1000 ps = 1ns
; OUTPUT CONTROL OPTIONS
nstxout = 0 ; save coordinates every 0 ps
nstvout = 0 ; save velocities every 0 ps
nstlog = 0 ; update log file every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstxtcout = 100000 ; Output frequency for xtc file
xtc-precision = 100000 ; precision for xtc file
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
pbc = xyz ; 3-D PBC
rlist = 1.0 ; short-range neighborlist cutoff
(in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff
(in nm)
rvdw = 1.0 ; short-range van der Waals cutoff
(in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for
long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
vdw-type = Cut-off
; T Coupling
Tcoupl = v-rescale ; modified Berendsen thermostat
tau_t = 0.1 ; time constant, in ps
ref_t = 290. ; reference temperature, one for
each group, in K
tc-grps = system
; P Coupling
Pcoupl = Berendsen; Parrinello-Rahman
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 5e-5
ref_p = 1.0
; Velocity generation
gen_vel = no
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; OPTIONS FOR BONDS
constraints = all-bonds ; all bonds constrained (fixed
length)
continuation = yes ; Restarting after NPT
constraint-algorithm = lincs ; holonomic constraints
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
Best regards
*Faezeh Pousaneh*
Best regards
*Faezeh Pousaneh*
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