[gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
Yu Ogawa
ayogwa at gmail.com
Fri May 23 21:34:06 CEST 2014
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
>>>>>>>> --
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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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