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

[Dan Sponseller]

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












> On Dec 31, 2014, at 3:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 12/31/14 3:05 PM, Dan Sponseller wrote:
>> Hello.
>> 
>> Every time I start a new simulation from a conformation that has been well equilibrated, there is a jump in the temperature. For example, starting from a .gro file with velocities that was a well equilibrated system at 400K has initial temperature about 440K.
>> 
>> I am not generating new velocities for the new simulation. This happens all the time. It is always about a 10% increase in the temperature.
>> 
>> Has anyone else experienced this? Does anyone know what might be happening?
>> 
> 
> Please post your full .mdp file; there are options relevant to proper continuation.  Also, velocities in .gro files are limited in precision.  It is much more reliable to restart using a checkpoint file (grompp -t *.cpt).
> 
> -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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