[gmx-users] simmulated annealing excess temperature........................
tarak20489 at gmail.com
Thu Aug 16 19:16:44 CEST 2012
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.
>> 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
>> 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
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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