[gmx-users] temperature problem
Justin Lemkul
jalemkul at vt.edu
Thu Jun 4 13:39:44 CEST 2015
On 6/4/15 12:39 AM, Lovika Moudgil wrote:
> Hi...Justin.... Thanks for explaining ...... I just want to ask could
> there be any other reasons too?? ...Because I have tried it with PME
> too...and still I am not getting desired temperature ....
>
You'll have to provide a full .mdp file and quantitative evidence of what you're
seeing. There are plenty of things that could be going on, but I'm not going
just blindly guess.
-Justin
>
>
> Thanks and Regards
> Lovika
>
>
> On Wed, Jun 3, 2015 at 5:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/3/15 3:46 AM, Lovika Moudgil wrote:
>>
>>> Hi...thanks for reply Peter and Mark ....I tried with temperature coupling
>>> . But things are still same ...
>>>
>>> Hi ... Mark would you like to explain this factor to me ??
>>>
>>>
>> Using a plain cutoff in the condensed phase is outdated methodology that
>> is very inaccurate. Cutoff artifacts lead to accumulation of heat in the
>> system. Use something sensible like PME.
>>
>> -Justin
>>
>>
>> Thanks and Regards
>>> Lovika
>>>
>>>
>>>
>>> On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>> Hi,
>>>>
>>>> Runaway heating is the only useful feature of cutoff electrostatics. Use
>>>> an
>>>> actual model physics.
>>>>
>>>> Mark
>>>>
>>>> On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon <p.c.kroon at rug.nl> wrote:
>>>>
>>>>
>>>>>
>>>>> On 02/06/15 09:43, Lovika Moudgil wrote:
>>>>>
>>>>>> Hi everyone
>>>>>>
>>>>>>
>>>>>> I am having some problem in my md run .In my system temperature of
>>>>>>
>>>>> system
>>>>
>>>>> is abruptly increasing .I have done nvt for 50 picoseconds ..nd then
>>>>>>
>>>>> using
>>>>>
>>>>>> it for further md simulation .I am not getting any error for this
>>>>>> temperature increase .....But when I plot temperature graph ,
>>>>>>
>>>>> temperature
>>>>
>>>>> is not same as nvt and is very high in md .I am having gold slab and
>>>>>>
>>>>> amino
>>>>>
>>>>>> acid in my system . Mdp file for md run is below ....Is their any error
>>>>>>
>>>>> in
>>>>>
>>>>>> my mdp file ???what could be the reason for this ???Please suggest ....
>>>>>> ; Run parameters
>>>>>> integrator = md ; leap-frog integrator
>>>>>> nsteps = 30000000 ; 2 * 50000 = 100 ps
>>>>>> dt = 0.001 ; 2 fs
>>>>>> ; Output control
>>>>>> ; Output control
>>>>>> nstxout = 500 ; save coordinates every 1.0 ps
>>>>>> nstvout = 500 ; save velocities every 1.0 ps
>>>>>> nstenergy = 500 ; save energies every 1.0 ps
>>>>>> nstlog = 500 ; update log file every 1.0 ps
>>>>>> nstxtcout = 500 ; [steps] freq to write
>>>>>>
>>>>> coordinates
>>>>>
>>>>>> to xtc trajectory
>>>>>> xtc_precision = 1000 ; [real] precision to write xtc
>>>>>> trajectory
>>>>>> xtc_grps = System ; group(s) to write to xtc
>>>>>> trajectory
>>>>>> energygrps = System ; group(s) to write to energy
>>>>>>
>>>>> file
>>>>>
>>>>>> ; Bond parameters
>>>>>>
>>>>>> constraint_algorithm = lincs ; holonomic constraints
>>>>>> constraints = all-bonds ; all bonds (even heavy
>>>>>> atom-H bonds) constrained
>>>>>> lincs_iter = 1 ; accuracy of LINCS
>>>>>> lincs_order = 4 ; also related to accuracy
>>>>>> ; Neighborsearching
>>>>>> cutoff-scheme = Verlet
>>>>>> ns_type = grid ; search neighboring grid cells
>>>>>> nstlist = 10 ; 20 fs, largely irrelevant with Verlet
>>>>>> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
>>>>>> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
>>>>>>
>>>>>> ; Electrostatics
>>>>>> coulombtype = cut-off
>>>>>> pme_order = 4 ; cubic interpolation
>>>>>> fourierspacing = 0.12 ; grid spacing for FFT
>>>>>> ; Temperature coupling is on
>>>>>> tcoupl = nose-hoover ; modified Berendsen
>>>>>>
>>>>> thermostat
>>>>>
>>>>>> tc-grps = Protein AUS AUB AUI SOL NA CL ; two coupling
>>>>>>
>>>>> groups -
>>>>
>>>>> more accurate
>>>>>> tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant,
>>>>>>
>>>>> in ps
>>>>>
>>>>>> ref_t = 300 300 300 300 300 300 300 ; reference
>>>>>> temperature, one for each group, in K
>>>>>>
>>>>> You have too many temperature coupling groups. (What Not To Do on
>>>>> http://www.gromacs.org/Documentation/Terminology/Thermostats)
>>>>> I'd stick to one for proteins, and one for the rest.
>>>>>
>>>>>> ; Pressure coupling is off
>>>>>> pcoupl = no ; no pressure coupling in NVT
>>>>>> ; Periodic boundary conditions
>>>>>> pbc = xyz ; 3-D PBC
>>>>>> ; Dispersion correction
>>>>>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>>>>> ; Velocity generation
>>>>>> ; Velocity generation
>>>>>> gen_vel = yes ; assign velocities from Maxwell
>>>>>>
>>>>> distribution
>>>>
>>>>> gen_temp = 300 ; temperature for Maxwell distribution
>>>>>> gen_seed = -1 ; generate a random seed
>>>>>>
>>>>>> ; To keep au surface in place, freeze Au atoms.
>>>>>> ; The AU group has been defined via make_ndx
>>>>>> ; to contains all the AU atoms ('a AU').
>>>>>> freezegrps = AUS AUB AUI
>>>>>> freezedim = Y Y Y Y Y Y Y Y Y
>>>>>> comm_mode = None
>>>>>>
>>>>>> Thanks and Reagrds
>>>>>> Lovika
>>>>>>
>>>>>
>>>>> Peter
>>>>>
>>>>>
>>>>> --
>>>>> 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 629
>> 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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>> 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 629
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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