[gmx-users] Effect of time step size

[Faezeh Pousaneh]

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*