[gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
Justin Lemkul
jalemkul at vt.edu
Fri May 23 20:01:12 CEST 2014
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_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.
>>>>>>>
>>>>>>> --
>>>>>> 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.
>>>>>
>>>>> --
>>>> 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.
>>>>
>>>>
>> --
>> ==================================================
>>
>> 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.
>>
--
==================================================
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
==================================================
More information about the gromacs.org_gmx-users
mailing list