Re: Restarting simulation goes the different temperature

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Apr 14 2008 - 10:18:08 CDT

Yes. You don't want to reinitialize the velocities when continuing a
simulation in progress.

On Apr 14, 2008, at 4:55 AM, Magnus Heltstrom wrote:

> 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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