[gmx-users] simmulated annealing excess temperature........................

[tarak karmakar]

Thanks a lot for the quick reply...................probably I  have
overlooked this point earlier
..........now I'm getting it properly........

On Thu, Aug 16, 2012 at 10:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/16/12 12:57 PM, tarak karmakar wrote:
>>
>> Dear All,
>>
>> In my simulation I want the temperature of the system to be reached at
>> 300 K only after 3 ps. But after 3ps I see temperature became 402 K.
>> So am I doing any mistake in the '.mdp' file given below?
>>
>
> You have a few.
>
> 1. You should not run MD with flexible water.
> 2. Finite cutoffs lead to rounding errors and accumulation of heat.  This is
> most likely the source of your problem.  I seem to recall Mark (or maybe
> someone else) already told you about this point.
>
> -Justin
>
>
>> define                = -DFLEXIBLE
>> constraints        = h-bonds
>> integrator          = sd
>> dt                        = 0.001          ; 1fs
>> nsteps               = 3000           ; 3ps
>> nstcomm           = 1
>> nstxout              = 1000           ; frequency to write coordinates
>> to output trajectory
>> nstvout              = 0              ; frequency to write velocities
>> to output trajectory; the last velocities are always written
>> nstfout               = 0              ; frequency to write forces to
>> output trajectory
>> nstlog                = 10             ; frequency to write energies to
>> log file
>> nstenergy         = 100 ; frequency to write energies to edr file
>> nstcalcenergy  = 100
>> vdwtype            = cut-off
>> coulombtype    = cut-off
>> pbc                    = no
>> table-extension   = 20.0
>> nstlist                    = 100
>> ns_type                = grid
>> rlist                        = 1.0
>>
>> rcoulomb           = 1.2
>> rvdw                   = 1.2
>>
>> comm-mode      = angular
>> comm-grps        = system
>> optimize_fft        = yes
>>
>> ;heating
>> annealing          = single
>> annealing_npoints      = 2
>> annealing_time           = 0 3
>> annealing_temp          = 0 300
>>
>> ld_seed                 = 8072012
>>
>> ;temperature coupling is on
>> Tcoupl = berendsen
>> tau_t = 0.01
>> tc_grps = system
>> ref_t = 0
>>
>> ;Pressure coupling is off
>> Pcoupl = no
>>
>> ; Generate velocites is on
>> gen_vel = yes
>> gen_temp = 0
>> gen_seed = 8042012
>>
>>
>>
>> Thanks,
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809