Great! My apologies for having missed that in the manual.
Thanks a lot!
Nikola
_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Carlos Simmerling
Sent: Thursday, June 07, 2007 3:42 PM
To: amber.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.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.scripps.edu [mailto: 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/ -
---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jun 10 2007 - 06:07:29 PDT
