[gmx-users] temperature problem
Lovika Moudgil
lovikamoudgil at gmail.com
Thu Jun 4 06:39:20 CEST 2015
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 ....
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 Using a plain cutoff in the condensed phase is outdated methodology that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
>>>>
>>>>
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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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