[gmx-users] Effect of time step size
Faezeh Pousaneh
fpoosaneh at gmail.com
Thu Feb 12 10:58:48 CET 2015
Dear Justin,
Thank you. Yes, both correspond to same setting except dt.
No, expected value is not known.
I have just tried to re-simulate with different values of lincs_itr and
lincs_order (2 and 8 respectively) and I get similar values for densities.
Could that be a good solution?
Best,
Best regards
*Faezeh Pousaneh*
On Wed, Feb 11, 2015 at 10:36 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
wrote:
> 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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