[gmx-users] Effect of time step size
Faezeh Pousaneh
fpoosaneh at gmail.com
Wed Feb 11 10:37:34 CET 2015
Dear Justin,
Thank you.
You are right about we must check validity of typologies attached in
Gromacs webpage, but I just took it for test of influence of 'time step' on
results when I was faced with similar problem in my own defined molecule. I
initially was simulating my Lutidine molecule, so let me please give
details of it, (running time 15 ns with same .mdp file as I sent before
except this time both with Parrinello-Rahman, 230 molecules in rectangular
box):
dt=0.002
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Temperature 289.953 0.03 5.63283 0.189132 (K)
Pressure 3.70721 2.6 389.728 -0.136095 (bar)
Density 956.957 0.67 8.57377 3.32218
(kg/m^3)
dt=0.001
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Temperature 289.994 0.033 5.70319 0.0487858 (K)
Pressure 1.82689 1.2 376.771 2.81752 (bar)
Density 967.363 0.58 8.21492 2.86186
(kg/m^3)
Yes, I let time for relaxation and I ignore those times before
equilibration. I do determine time-dependence of parameters like density
and etc, but also I check RMSD of lutidine-lutidine in order to carefully
collect the data which are stable. But as you see still there are
difference in densities? Isn't is big difference?
Many thanks
Best regards
*Faezeh Pousaneh*
On Tue, Feb 10, 2015 at 9:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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