[gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
Mark Abraham
mark.j.abraham at gmail.com
Sat May 24 03:56:04 CEST 2014
To say nothing of the fact that the manual clearly states MTTK is not
useable with the md integrator. But who reads manuals these days? :-)
Mark
On Fri, May 23, 2014 at 9:49 PM, Thomas C. O'Connor <toconnor at jhu.edu>wrote:
> 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
> > >>>>>>>>
> > >>>>>>>> * Please search the archive at
> > >>>>>>>>
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore
> > >>>>>>>> posting!
> > >>>>>>>>
> > >>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>>>>
> > >>>>>>>> * For (un)subscribe requests visit
> > >>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> > >>>>>>>> gmx-usersor
> > >>>>>>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>>>>>
> > >>>>>>>> --
> > >>>>>>>>
> > >>>>>>> Gromacs Users mailing list
> > >>>>>>>
> > >>>>>>> * Please search the archive at
> > >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore
> > >>>>>>> posting!
> > >>>>>>>
> > >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>>>
> > >>>>>>> * For (un)subscribe requests visit
> > >>>>>>>
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > >>>>>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>>
> > >>>>>> Gromacs Users mailing list
> > >>>>>>
> > >>>>>> * Please search the archive at
> > >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore
> > >>>>>> posting!
> > >>>>>>
> > >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>>
> > >>>>>> * For (un)subscribe requests visit
> > >>>>>>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > >>>>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>>>
> > >>>>>> --
> > >>>>>>
> > >>>>> Gromacs Users mailing list
> > >>>>>
> > >>>>> * Please search the archive at
> > >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >>>>> posting!
> > >>>>>
> > >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>
> > >>>>> * For (un)subscribe requests visit
> > >>>>>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > >>>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>>
> > >>>>>
> > >>>>> --
> > >>> ==================================================
> > >>>
> > >>> 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
> > >>>
> > >>> ==================================================
> > >>>
> > >>> --
> > >>> Gromacs Users mailing list
> > >>>
> > >>> * Please search the archive at http://www.gromacs.org/
> > >>> Support/Mailing_Lists/GMX-Users_List before posting!
> > >>>
> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>
> > >>> * For (un)subscribe requests visit
> > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > >>> send a mail to gmx-users-request at gromacs.org.
> > >>>
> > >>>
> > > --
> > > ==================================================
> > >
> > > 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
> > >
> > > ==================================================
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list