AMBER Archive (2003)

Subject: RE: AMBER: Not getting restrt file on running sanders

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Oct 09 2003 - 18:25:11 CDT

Hello,

ntwr applies to dynamics not minimization.
A restart file is written every NSTLIM steps for both
dynamics and minimization.

When I tried your input, after decreasing the surprisingly large
maxcyc to 700, using the prmtop and inpcrd from test/ubiquitin,
a restart file was written at step 700.
Without knowing the details of your system it is recommended
that maxcyc be reduced by a couple of orders of magnitude.

Scott

On Thu, 9 Oct 2003, Asim Okur wrote:

> To be able to write a restrt file you have to use ntwr in the input
> file.
>
> ntwr = 10
>
> will write to the restart file every 10 steps,
>
> Asim Okur
>
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Vikas Varshney
> Sent: Thursday, October 09, 2003 5:40 PM
> To: amber_at_scripps.edu
> Subject: AMBER: Not getting restrt file on running sanders
>
> Dear AMBER users,
> I tried to run minimization of a system of around 500 residues (~5000
> atoms) in
> sander with option -r restart, but did not get the restart file. Here is
> my input file.
> Minimization
> &cntrl
> imin=1,maxcyc=100000,ntmin=2,
> ntpr=10,iwrap=1,
> &end
> Group input for restrained atoms
> 2.0
> RES 383 478
> END
> END
>
> I will really appreciate if you are can help me with this.
>
> Many regards and thanks,
>
> VIkas Varshney
> Dept. of polymer science
> University of Akron.
>
>
> <http://clients.rediff.com/signature/track_sig.asp>
>

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