[gmx-users] Jump in temperature each time a new simulation is started.

[Justin Lemkul]

On 12/31/14 7:22 PM, Dan Sponseller wrote:
> Thank you for getting back to me. I understand the limited precision of the .gro file but it cannot explain such a large jump in the temperature. Other than the fact that I am starting a new simulation, the parameters in the .mdp file are the same as the ones that equilibrated and produced the .gro file. Below is my .mdp file.
>
> Thank you again.
>
> Daniel Sponseller
> PhD Candidate
> George Mason University
>
>
>
> ; This mdp file is for an NPT ensemble.
>
> ** Run Control **
> integrator               = md
> dt                       = 0.00005
> nsteps                   = 700000
> comm-mode                = Linear
> nstcomm                  = 50
>
> ** Output Control **
> nstxout                  = 10000
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 1000
> nstcalcenergy            = 20
> nstenergy                = 20
> energygrps               = System
>
> ** Neighbor Searching **
> cutoff-scheme            = Verlet
> nstlist                  = 40
> nstcalclr                = -1
> ns_type                  = grid
> pbc                      = xyz
> periodic-molecules       = no
> rlist                    = 4.0
> rlistlong                = -1
> verlet-buffer-drift      = -1
>
> ** Electrostatics **
> coulombtype              = PME
> coulomb-modifier         = Potential-shift
> rcoulomb                 = 3.8
>
> ** VdW **
> vdwtype                  = Cut-off
> vdw-modifier             = Potential-shift
> rvdw                     = 3.8
>
> ** Ewald **
> fourierspacing           = 0.15
> pme-order                = 6
> ewald-rtol               = 1e-5
>
> ** Temperature Coupling **
> tcoupl                   = v-rescale
> nsttcouple               = -1
> tc-grps                  = System
> tau-t                    = 1.0
> ref-t                    = 400
>
> ** Pressure Coupling **
> ;pcoupl                   = no
> pcoupl                   = berendsen
> pcoupltype               = isotropic
> nstpcouple               = -1
> tau-p                    = 2.0
> compressibility          = 4.5e-5
> ref-p                    = 1
> refcoord-scaling         = all
>
> ** Velocity Generation **
> gen-vel                  = no
> gen-temp                 = 400
> gen-seed                 = 4242
>
> ** Bonds **
> constraints              = none
> morse                    = yes
>

Are there any constraints defined in the topology?

Do the velocities in the .tpr file (from gmxdump) agree with the velocities in 
the .gro file?  Does the problem go away if you supply grompp -t with the 
checkpoint from the previous run?

-Justin

-- 
==================================================

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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