Re: restarting files converge to new temperature

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Feb 13 2008 - 10:13:55 CST

Hi Jorgen,
very large variations in instantaneous pressure are normal -- see the
section in the namd manual on pressure control
(http://www.ks.uiuc.edu/Research/namd/2.6/ug/node32.html) for why.
Best,
Peter

Jorgen Simonsen wrote:
> Hi,
>
> thanks for the answer - it seems stable now. I have look at my
> pressure if I plot the pressure of the log file I get a normal
> distribution with a mean of 1.013 but a huge variance and if I plot
> with the values pressavg or gpressavg I get the same mean and still a
> large standard deviation(44) - is it normal to have such a large SD on
> the pressure?
> I pressume to be in the NPT ensemble with some noise do to the
> langevin stochastics noise.....
>
> Any advise appreciated - thanks
>
>
> On Feb 13, 2008 2:55 PM, Peter Freddolino <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> 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>
> > <mailto: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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