Re: two stage equilibration in single configuration file

From: Bassam Haddad (
Date: Thu Aug 03 2017 - 12:29:53 CDT

If you want to just start it up and run it without having to check on it
you can just write a simple bash script. You just have to prepare both
configuration files beforehand.

>echo "Beginning initial equilibration with the protein constrained."
>namd2 +p(N) first_equil.conf > first_equil.out &
>echo "Initial equilibration has finished."
>echo "Beginning second equilibration."
>namd2 +p(N) second_equil.conf > second_equil.out &
>echo "Equilibration has finished"


On Thu, Aug 3, 2017 at 9:38 AM, Vermaas, Joshua <>

> I'm pretty sure the answer is no. You'd need to turn the protein
> restraints on, run for a few thousand steps, and then turn the
> restraints off. I'm pretty sure the config file parser won't let you do
> this without an error. It isn't a big deal, since you can just do it in
> two parts.
> -Josh
> On 08/03/2017 12:10 AM, wrote:
> > I want to carry out a two stage equilibration in the first stage i don't
> > want my protein to move only the water molecules will take part in the
> > dynamics and in the second stage whole system will equilibrate,my
> question
> > is that can it be done in a single configuration file?
> >
> >

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