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

[Justin Lemkul]

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,
>

-- 
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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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