AMBER Archive (2007)

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

From: Nikola Trbovic (nt2146_at_columbia.edu)
Date: Thu Jun 07 2007 - 14:54:35 CDT

Great! My apologies for having missed that in the manual.

 

Thanks a lot!

 

Nikola

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Carlos Simmerling
Sent: Thursday, June 07, 2007 3:42 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: extracting starting structures from equilibration
trajectory

 

yes- page 91 of the amber9 manual. set ntwr to a negative value.

On 6/7/07, Nikola Trbovic <nt2146_at_columbia.edu > 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
<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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