Re: Defining Temperature for Langevin for Namd restart.

From: Amr Zeinalabideen Majul (amajul_at_gmu.edu)
Date: Wed Aug 05 2009 - 16:20:41 CDT

Thanks for the reply,

the reason I asked was because I got a Fatal error when I commented out the langevinTemp. I also took care of thelangevinPistonTemp $temperature line.

Your reply leads me to believe that I must have something else wrong in the configuration file, probably I did something wrong in redefining my Periodic Boundary conditions.

I will look over it and if I can't figure it out I will post the config file.

Thanks,
Amr Majul

----- Original Message -----
From: Roman Petrenko <rpetrenko_at_gmail.com>
Date: Wednesday, August 5, 2009 4:13 pm
Subject: Re: namd-l: Defining Temperature for Langevin for Namd restart.

> just comment out one line
> langevinTemp ....
>
> also in namd somewhere comment out something like
> temperature ....
>
> temperature value is "hidden" in the atomic velocities, so, yes it is
> computed back from velocities on restarts.
>
>
> On Wed, Aug 5, 2009 at 3:20 PM, Amr Zeinalabideen
> Majul<amajul_at_gmu.edu> wrote:
> > Hello all,
> >
> > Im trying to continue a simulation of a peptide in water, which I
> have run for 200 picoseconds, and wish to continue the simulation
> for 200 more seconds.
> >
> > All the example files out there are very clear about commenting
> out the initial setting of the velocity temperature, so I have the
> following:-
> >
> > #############################################################
> > ## ADJUSTABLE PARAMETERS                                   ##
> > #############################################################
> >
> > structure          sp1_wb.psf
> > coordinates        sp1_wb.pdb
> > bincoordinates     sp1_output.restart.coor
> > binvelocities      sp1_output.restart.vel
> >
> > # set temperature    310
> > set outputname     sp1_400_wb
> >
> > firsttimestep      100100
> >
> > So now how do I deal with the langevinTemp variable under
> Temperature Control?
> >
> > # Constant Temperature Control
> > langevin            on    ;# do langevin dynamics
> > langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
> > langevinTemp        $temperature
> > langevinHydrogen    off    ;# don't couple langevin bath to
> hydrogens>
> > If I comment it out, will ti automatically use the temperature in
> the .vel file? Or do I have to define the langevinTemp to be the
> temperature in the .vel file?
> >
> > Thanks in advance
> >
> > Amr Majul
> >
> >
>
>
>
> --
> Roman Petrenko
> Physics Department
> University of Cincinnati
>
>

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