AMBER Archive (2005)

Subject: Re: AMBER: Error in "restrt" output file

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Wed Sep 14 2005 - 16:41:41 CDT

> From: Alexander Rubinstein <arubin_at_unmc.edu>
>
> I would like to carry out a long time high temperature MD simulation for
...
>
> md_52_Ab40_WN.xyz (restrt file):
>
> line 3254>310.0074935 299.7106465 -96.1944303 116.7414444 -30.3483541************
> 116.4267112 -31.2457463************ 116.9960680 -30.0752141************

The precision of the trajectory and restart files is not large; if your
coordinates (in this case) exceed 9999.9999999 or -999.9999999, you blow
the FORTRAN format statement and *****'s are output. This can happen due
to normal translation of the molecules. In explicit periodic solvent, you
can avoid this by imaging (IWRAP=1). In gas phase (and also in periodic
simulation), it can be necessary to removing the center of mass
translation of the entire system periodically (NSCM=500). If you are
doing explicit non-periodic solvent, you may be out of luck without
applying a cap potential since the water can freely diffuse away. Based
on what you reported, simply setting IWRAP=1 should do it, but note that
the trajectory file is even less precise than the restart so these will be
corrupted earlier than the restart file...

--tom

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham
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