Re: restarting files converge to new temperature

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Feb 13 2008 - 07:55:48 CST

Hi Jorgen,
the only information the restart files contain is the coordinates,
velocities, and periodic cell size/strain rate. If you want to keep your
simulation under temperature/pressure control, you do need to include
those portions in subsequent restart files. The
temperature $temperature
line needs to be commented out because it only provides a temperature
for the initial velocity distribution, which is not needed if you have a
velocity restart file.
Best,
Peter

>
>
> should I include the barostat and thermostat as well in the restart-file?
>
> ####### PRES CONTROL
> langevinPiston on
> # Appling the langevinpiston for pressure control
> langevinPistonTarget 1.01325
> # One atomsheric pressure at sea level
> langevinPistonPeriod 100
> # barostat oscillation time scale for LP method
> langevinPistonDecay 50
> # barostat damping time scale for LP
> LangevinPistonTemp $temperature
> # barostat noise temperature for LP
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigid bonds
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, maybe for membrane
> ####### TEMP CONTROL
> langevin on
> # langevin dynamics
> langevinDamping 5.
> # damping coefficient of 5/ps
> langevinTemp $temperature
> # Random noise at this level
> langevinHydrogen no
> # Do not couple bath to hydrogens
>
> should this be included as well with the $temperature commented out?
> Any help or advise appreciated -
> thanks in advance
> Best
>
>
>
>
>
>
>
>
> On Feb 12, 2008 8:34 PM, Peter Freddolino <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> Hi Jorgen,
> are you running with temperature control? It isn't apparent from your
> config file.
> Best,
> Peter
>
> Jorgen Simonsen wrote:
> > Hi,
> >
> > I had a crash with the MD run and would like to restart the
> > calculation. I use the restart files first with the extension
> *.coor,
> > *.vel, *.xsc which gave an error that it could read the *.coor. I
> > moved the files *.coor.old, *.vel.old, *.xsc.old into *.coor,
> *.vel,
> > *.xsc and restarted the calculation - the problem is that instead of
> > using a temperature of 300 K it is now using a temperature of around
> > 270 K. How to resolve this and what is the problem?
> > Any help or advise appreciated - thanks in advance
> >
> > Best
> > J
> >
> > # Restarting simulation
> > set inputname min_whole_sys
> >
> > Bincoordinates $inputname.restart.coor
> > Binvelocities $inputname.restart.vel
> > ExtendedSystem $inputname.restart.xsc
> >
> > #########################################################
> > proc get_first_ts { xscfile } {
> > set fd [open $xscfile r]
> > gets $fd
> > gets $fd
> > gets $fd line
> > set ts [lindex $line 0]
> > close $fd
> > return $ts
> > }
> >
> > set firstts [get_first_ts $inputname.restart.xsc]
> >
>
>

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