[gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
Yu Ogawa
ayogwa at gmail.com
Fri May 23 19:33:12 CEST 2014
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
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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