# [gmx-users] Effect of time step size

Justin Lemkul jalemkul at vt.edu
Tue Feb 10 21:49:50 CET 2015

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On 2/10/15 3:41 PM, Faezeh Pousaneh wrote:
> 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.
>

RMSD of what?  I doubt that analysis of any value here.  You should determine
the time-dependence of quantities of interest, like diffusion constant, density,
etc.

> 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?
>

These are single numbers without error estimates, so there's nothing to be said.
If both values are +/- 20, then there's probably no difference.  Are you
allowing time for relaxation, or are you including all frames (thus some
unequilibrated time)?

> 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?
>

What topology is that?  I see methanol for download, but not ethanol.  What is
the reference for the parameters?  If there isn't one, I'd be skeptical about
using it.  Find a model that has a known (expected) density value, and make sure
you can reproduce it using sensible run settings.  Note too that "from the
GROMACS homepage" doesn't necessarily imply validity; the user contributions are
provided as a convenience but there is no endorsement of correctness; that's for
you to evaluate based on publications and your own assessments.

>   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

The Berendsen algorithm does not yield a correct ensemble.  Use Parrinello-Rahman.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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