Thanks for the effort anyway!
Best,
Nikola
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Ilyas Yildirim
Sent: Thursday, June 07, 2007 3:58 PM
To: amber.scripps.edu
Subject: RE: AMBER: extracting starting structures from equilibration
trajectory
Just ignore this email. Carlos Simmerling's solution (which is part of
amber) is better than this.
On Thu, 7 Jun 2007, Ilyas Yildirim wrote:
> 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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of
> > Ilyas Yildirim
> > Sent: Thursday, June 07, 2007 2:14 PM
> > To: amber.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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Received on Sun Jun 10 2007 - 06:07:29 PDT
