Re: Restarting simulation goes the different temperature

From: Magnus Heltstrom (mheltstrom_at_gmail.com)
Date: Mon Apr 14 2008 - 04:55:57 CDT

Hi,

Thanks for the answer so by removing the reinitvels it should stay at the
specified temperature?

Best and many thanks

On Thu, Mar 6, 2008 at 2:08 AM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> Do you have minimize or possibly reinitvels in your config file?
>
> Also, firsttimestep is actually a command (flag?), not a variable, so you
> don't use set before it.
>
>
>
> On Mar 5, 2008, at 10:19 AM, Magnus Heltstrom wrote:
>
> Hi,
> >
> > I try to restart my calculation but the temperature has changed from ~
> > 301 K to 201 K. The temperature raises for the next 20.000 steps and
> > equilibrate around 294 K which should be 300 K. This I find rather
> > strange..... My restart file looks like this
> >
> > # Restarting simulation
> > set inputname sys
> >
> > Bincoordinates $inputname.restart.coor
> > Binvelocities $inputname.restart.vel
> > ExtendedSystem $inputname.restart.xsc
> >
> > etc etc
> > ........
> > etc etc
> >
> >
> > set firsttimestep 8312000
> >
> > langevin on
> > langevinDamping 5.
> > langevinTemp 300
> > langevinHydrogen no
> >
> > langevinPiston on
> > langevinPistonTarget 1.01325
> > langevinPistonPeriod 100
> > langevinPistonDecay 50
> > LangevinPistonTemp 300
> > useGroupPressure yes ;# needed for rigid bonds
> > useFlexibleCell no ;# no for water box, yes for membrane
> > useConstantArea no ;# no for water box, maybe for membrane
> >
> >
> > wrapWater on
> > wrapAll on
> >
> > PME yes
> > PMEGridSizeX 64 ;
> > PMEGridSizeY 64 ;
> > PMEGridSizeZ 64 ;
> >
> > run $md
> >
> > If I look into the output file I get the following informations
> >
> > Info: EXTENDED SYSTEM FILE min_whole_sys.restart.xsc
> > Info: VELOCITY FILE min_whole_sys.restart.vel
> > Info: BINARY COORDINATES min_whole_sys.restart.coor
> >
> > I start up with
> >
> > Info: RANDOM NUMBER SEED 1204732890
> >
> >
> > How to resolve this and what is the problem? Furthermore, I try to set
> > the firsttimestep 8312000 but the log file starts at 0...
> >
> > Any help or advise appreciated - many thanks.
> >
> > Best Mag
> >
>
>

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