AMBER Archive (2007)

Subject: RE: AMBER: extracting starting structures from equilibration trajectory

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Jun 07 2007 - 14:54:06 CDT

You can write a script which will search the files in a directory once in
a while (let's say once in 2 minutes), and save the .rst file. You
will run this script while your sander job is running. Other than
that, I dont think that sander has an option to save the .rst files the
way u ask.

On Thu, 7 Jun 2007, Nikola Trbovic wrote:

> Thanks for the quick reply!
>
> Is there perhaps a way to save .rst files at regular intervals during the
> equilibration run in a way that they are not overwritten?
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Ilyas Yildirim
> Sent: Thursday, June 07, 2007 2:14 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: extracting starting structures from equilibration
> trajectory
>
> The .mdcrd files do not store any velocity information. So, when u extract
> the restart files from a .mdcrd file using ptraj, they wont have any
> velocity information in them. As a result, u need to re-equilibrate each
> system. Only .rst files have velocity info. in them.
>
> On Thu, 7 Jun 2007, Nikola Trbovic wrote:
>
> > Dear all,
> >
> >
> >
> > I'm trying to use snapshots from an NPT equilibration trajectory as
> starting
> > structures for several NVE production runs. I tried extracting snapshots
> as
> > Amber restart files from the equilibration trajectory as follows:
> >
> >
> >
> > ptraj prmtop << EOF
> >
> > trajin equi.mdcrd 300 1000 100
> >
> > trajout start restart
> >
> > EOF
> >
> >
> >
> > This produces 8 restart files from the equilibration trajectory, just like
> I
> > want it to. But when I start the production runs with irest=1 and ntx=5,
> the
> > temperature starts out around 190K, although it is clearly equilibrated at
> > 300K in the time window of the NPT equilibration trajectory that I
> specified
> > for extracting the starting structures by ptraj. How do I fix this?
> >
> >
> >
> > Thanks a lot in advance for any suggestions,
> >
> > Nikola
> >
> >
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemistry      -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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