[gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
Thomas C. O'Connor
toconnor at jhu.edu
Fri May 23 22:07:26 CEST 2014
I might just add:
Your time-scale for controlling your thermostat (tau_t) is set equal to
your timescale time-scale for controlling your barostat (tau_p). Having
these two relaxation times set equal can be quite unstable, especially if
your system is not already in equilibrium.
You typically want your tau_p to be larger (how much varies but ~ a factor
of 10 is safe) than your tau_t. This is because you want the thermal
degrees of freedom to be well equilibrated much faster than the system box
changes size.
The value of time constants that produce stable simulations also depends on
your system. A couple of good rules of thumb for tau_t and tau_p would be:
1. Choose tau_t > than the intermolecular collision time of your system.
(This can be determined from a calculation of the velocity autocorrelation
function).
2. Choose tau_p so that it is larger than the sound transit time of your
system.. i.e. make tau_p larger than the time needed by a sound wave to
travel across your system. This is because the fluctuations in density
caused by changing the simulation box size need to dissipate and correlate
throughout the system and they do so at ~ the speed of sound.
I hope this helps. Thermo/Barostating can be really frustrating and cause
a lot of headaches if your time-scales aren't right!
-Thomas
On Fri, May 23, 2014 at 3:10 PM, Yu Ogawa <ayogwa at gmail.com> wrote:
> Dear Justin,
>
> Thank you very much for your advice.
> Okay, I will try according to your procedure.
>
> Yu
>
>
> 2014-05-23 19:48 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 5/23/14, 1:26 PM, Yu Ogawa wrote:
> >
> >> This is my mdp file.
> >>
> >> ;define = -DFLEX_SPC
> >> constraints = none
> >> ;constraint_algorithm = LINCS
> >> integrator = md
> >> dt = 0.0005 ;ps !
> >> nsteps = 100000000 ; total 50 ns.
> >> nstcomm = 2
> >> nstxout = 10000
> >> nstvout = 10000
> >> nstfout = 0
> >> nstlog = 10000
> >> nstenergy = 10000
> >> nstlist = 5
> >> ns_type = grid
> >> coulombtype = PME
> >> rlist = 0.9
> >> rcoulomb = 0.9
> >> rvdw = 0.9
> >> ; Berendsen temperature coupling is on in two groups
> >> Tcoupl = nose-hoover
> >> tau_t = 0.1
> >>
> >> tc-grps = GLC
> >> ref_t = 5
> >> annealing = single
> >> annealing_npoints = 109
> >> annealing_time = 0 200 800 1000 1600 ... 41200 41800 42000 42600
> >> 42800
> >> annealing_temp = 5 20 20 40 40 ... 40 40 20 20 0
> >>
> >> Pcoupl = MTTK
> >> tau_p = 0.1
> >> pcoupltype = anisotropic
> >> compressibility = 1e-5 1e-5 1e-7 1e-5 1e-5 1e-5
> >> ref_p = 1.0 1.0 1.0 0 0 0
> >> gen_vel = yes
> >> gen_temp = 5
> >> gen_seed = 173529
> >> pbc = xyz
> >> periodic_molecules = yes
> >> DispCorr = EnerPres
> >> optimize_fft = yes
> >>
> >>
> > Generating new velocities with Nose-Hoover can be very unstable; grompp
> > should have thrown a warning about this. You should equilibrate for a
> > while at the starting temperature, then pass the .cpt file from the
> > equilibration to the annealing run to preserve the previous ensemble.
> > Re-generating velocities negates any equilibration done previously, and
> > whether or not the simulation works is, at that point, a bit of a
> coin-flip.
> >
> > -Justin
> >
> >
> >
> >> 2014-05-23 19:07 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
> >>
> >>
> >>>
> >>> On 5/23/14, 1:02 PM, Yu Ogawa wrote:
> >>>
> >>> Sorry for my poor explanation. I tried to simulate a temperature
> rising
> >>>> process from 0 K to 500 K.
> >>>> At first I did a simulation with gen_vel=no, and the temperature was
> >>>> just
> >>>> around 3 to 5 K and never rose up. then I tried to give a velocities
> >>>> with
> >>>> gen_temp though I don't know if it's correct or not.
> >>>>
> >>>>
> >>>> You'll need to post complete .mdp files of whatever it is you're
> doing.
> >>> Trying to provide help based on fragmented information is very hard,
> >>> and
> >>> it could be a simple matter of some incorrect settings, but we can't
> >>> tell.
> >>>
> >>> -Justin
> >>>
> >>>
> >>>
> >>>
> >>>> 2014-05-23 18:42 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
> >>>>
> >>>> What has gen_temp to do with it? You sound like you're doing an
> >>>>
> >>>>> equilibration, then generating velocities at gen_temp, then running
> >>>>> with
> >>>>> a
> >>>>> thermostat with a different ref_t from gen_temp. Why?
> >>>>>
> >>>>> Mark
> >>>>>
> >>>>>
> >>>>> On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa <ayogwa at gmail.com> wrote:
> >>>>>
> >>>>> Dear Mark,
> >>>>>
> >>>>>>
> >>>>>> At the very last part of the log file I can find outputs at 0.0 ps,
> >>>>>> but
> >>>>>> nothing more below.
> >>>>>>
> >>>>>> Have you equilibrated your system first? Does another integrator
> or
> >>>>>>
> >>>>>>>
> >>>>>>> thermostat work?
> >>>>>>
> >>>>>> Yes, my mdrun program works with the other inputs, and I think the
> >>>>>>
> >>>>>> initial
> >>>>>
> >>>>> structure is equilibrated enough because I can run a NPT simulation
> >>>>>> properly with this structure file with md integrator and berendsen
> >>>>>> thermostat.
> >>>>>>
> >>>>>> I also tried the similar calculation with md integrator and
> >>>>>> Nose-Hoover.
> >>>>>>
> >>>>>> In
> >>>>>
> >>>>> this case I could start running the simulation, but the temperature
> >>>>>> was
> >>>>>>
> >>>>>> not
> >>>>>
> >>>>> controlled, and it stayed around the value of gen_temp.
> >>>>>>
> >>>>>> Thank you,
> >>>>>> Yu
> >>>>>>
> >>>>>>
> >>>>>> 2014-05-23 16:33 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
> >>>>>>
> >>>>>> First, find something out. Does the installation work for any
> other
> >>>>>>
> >>>>>>> simulation? What does the log file say? Have you equilibrated your
> >>>>>>>
> >>>>>>> system
> >>>>>>
> >>>>>
> >>>>> first? Does another integrator or thermostat work?
> >>>>>>
> >>>>>>>
> >>>>>>> Mark
> >>>>>>>
> >>>>>>>
> >>>>>>> On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa <ayogwa at gmail.com>
> wrote:
> >>>>>>>
> >>>>>>> Hello gmx-users,
> >>>>>>>
> >>>>>>>>
> >>>>>>>> I tried to run a simulation to calculate a specific heat capacity
> of
> >>>>>>>> infinite molecular crystal with the md-vv integrator and
> Nose-Hoover
> >>>>>>>> thermostat on ver 4.6,
> >>>>>>>> but it crashed immediately with only the message of Segmentation
> >>>>>>>>
> >>>>>>>> fault.
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>>>
> >>>>>>>> Does anyone have a similar experience or any good ideas for this
> >>>>>>>>
> >>>>>>>> problems?
> >>>>>>>
> >>>>>>>
> >>>>>>>> I would appreciate very much if somebody gives any comments on
> this
> >>>>>>>>
> >>>>>>>> matter.
> >>>>>>>
> >>>>>>> Thank you,
> >>>>>>>>
> >>>>>>>> Yu
> >>>>>>>>
> >>>>>>>> Yu OGAWA, PhD
> >>>>>>>> Cermav-CNRS, Grenoble, France
> >>>>>>>> --
> >>>>>>>> Gromacs Users mailing list
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> >>>>> --
> >>> ==================================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>
> >>> Department of Pharmaceutical Sciences
> >>> School of Pharmacy
> >>> Health Sciences Facility II, Room 601
> >>> 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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> >>>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > 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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--
Thomas O'Connor
Graduate Research Assistant
MCS IGERT Fellow
Department of Physics & Astronomy
The Johns Hopkins University
3701 San Martin Drive
Baltimore, MD 21218*toconnor at jhu.edu <toconnor at jhu.edu>*410.516.8587
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