AMBER Archive (2004)

Subject: Re: AMBER: a question on ntwx and ntwr

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Oct 28 2004 - 10:50:10 CDT

since the restart file has a time in it, and you know how often you
write trajectory
frames, you can easily find out of the trajectory has too many frames.
you can
then use ptraj to extract only the frames you want using the trajin command.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

scopio wrote:

> Dear AMBER users:
>
> I wonder what will happen to the trajectory file if restarting a
> broken MD calucation when ntwx is less than ntwr?
> Since that ntwr is the step length for writting restart coordinate
> file and ntwx is the step length for writting trajectory file, we can
> consider that if ntwx is less than ntwr, it is possible the trajectory
> has more frames recorded beyond the point of restart file when the
> calcuation is broken. Thus when we restart this calucation, there
> must have some duplicated portions between the old trajctory and the
> newly trajcetory started from the point of restart file recorded, if
> no modification applied on the previous trajctory. If this is right,
> the time value in the plot of flucutation vs time might be incorrect.
>
> Best Regards!
>
> Liu

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