Subject: Re: CCL:Questions about CHARMM I/O

From: Rick Venable <rvenable=at=pollux.cber.nih.gov>
Date: Fri, 9 Jul 2004 16:06:48 -0400

Reminder: try the CHARMM Forums at www.charmm.org for questions about
using academic CHARMM.

(Questions about using the commercial CHARMm product via Quanta or
InSight should be directed to Accelrys).

On Fri, 9 Jul 2004 h9807907=at=hkusua.hku.hk wrote:
> I am new to CHARMM and I hope that you can give me some ideas of the following
> questions.
> 1) Do anyone know how to print out the coordinate file and restart file at
> different time intervals during a MD similation? Is that possible by modifying
> the .inp file?

The coordinates are saved in the trajectory file indicated by IUNCRD
every NSAVC integration steps; change NSAVC to change the frequency for
saving coordinate sets.

By default, the restart file is only written once, at the end of the
run; for modern computer systems with low failure rates, this is the
preferred method.  The ISVFRQ option of DYNAmics can be used to write
the restart file (to the unit specified by IUNWRI) more often.

> 2) How can I suppress the print of those files, such as .vel .ene, which I
> cannot read?

Don't open the files and assign unit numbers, and don't specify a
frequency (in integration steps) for these, i.e. the DYNAmics command
would include

	IUNVEL -1 NSAVV 0  KUNIT -1

The .ene file should be readable, just not easily understood.

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Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   Rick_Venable=at=nih.gov
ALT email:  rvenable=at=speakeasy.org
-------------------------------------
"Don't blame me, I voted for Kang."
                         Homer
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