[gmx-users] Effect of time step size
Faezeh Pousaneh
fpoosaneh at gmail.com
Tue Feb 10 21:41:45 CET 2015
Dear Mark,
Thank you so much for the reply.
I had sent the .mdp file in my previous email (below). In more details I
had equilibriuted 1728 methanol (NPT ensemble at T=290 and P=1atm, using
all-bond constraint) for long enough time (10 ns) and I am sure I have
reached the equilibrium according to RMSD analysis.
1- You are right about time step with constraint, however I have been
running for dt=0.002 as well, and I get density 790 kg/m^3. it means that
still there is a big difference in result of dt=0.001 and dt=0.002:
> 783 kg/m^3 for dt=0.001
> 790 kg/m^3 for dt=0.002
isn't big difference? then how it is said that dt can be at most 0.002?
2- I see that in the experiment the density of ethanol is 791 Kg/m^3 at
T=290. That is not in agreement with my result for dt=0.001. What does it
mean? does it mean that the given topology of ethanol (I take it from
Gromacs homepage) is not well defined?
integrator = md
dt = 0.001
nsteps = 10000000
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 ;
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
Many thanks in advance.
------------------
Best regards
*Faezeh Pousaneh*
On Tue, Feb 10, 2015 at 6:33 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> On Tue, Feb 10, 2015 at 12:16 PM, Faezeh Pousaneh <fpoosaneh at gmail.com>
> wrote:
>
> > 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?
> >
>
> One needs to have sampled long enough to have reached equilibrium and then
> made enough observations for a sensible average. You haven't told us what
> you've done there, so we'll have to assume that. The size of the time step
> is closely tied to the model physics - you want to have a healthy number of
> time steps per fastest motion in the system, which for atomistic MD with
> some kind of bond constraints normally is at most 2fs. See manual section
> on removing fast motions for some details. So if dt=3fs is reproducibly
> wrong, then it looks like a case of garbage in = garbage out.
>
> Mark
>
>
> > 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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