From owner-chemistry ^at^ ccl.net Tue Jul 28 02:45:01 2009
From: "Nicolas Staelens nicolas.staelens###fundp.ac.be" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: Tinker dynamic function strange data
Message-Id: <-39860-090728022409-5992-n67QbyD0vnnDcvlrLjPkSw::server.ccl.net>
X-Original-From: Nicolas Staelens <nicolas.staelens##fundp.ac.be>
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Date: Tue, 28 Jul 2009 07:46:06 +0200
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Sent to CCL by: Nicolas Staelens [nicolas.staelens~!~fundp.ac.be]
Hello,

Did you try performing a quick geometry optimisation prior to running =20=

the Dynamic function? Maybe there are atoms too close to each other, =20
which can result in troubles with that function.

Have a nice day

Nicolas Staelens

Ph. D. Student
PCI Laboratory
University of Namur
Belgium

Le 28 Jul 2009 =E0 01:00, Ron Salesky rsalesky%unm.edu a =E9crit :

>
> Sent to CCL by: "Ron  Salesky" [rsalesky:_:unm.edu]
> Is anyone on this list familiar with Tinker's dynamic function? =20
> Please note that this should supersede an earlier request posted on =20=

> this board as it describes more accurately and in greater detail the =20=

> issue at hand.
>
> I get very strange results as follows:
>
> 1. Without using a periodic box, the Cartesian coordinates 'dump' =20
> file contains either ****** for some coordinates and outlandish =20
> coordinate values for other coordinates, e.g. 46000.0 angstroms =20
> where the largest value in the input coordinates file was 20 =20
> angstroms. The input file contains ~4600 atoms
>
> OR
>
> 2. If a periodic box is defined in the key file, it simply never =20
> runs... several text output lines were placed in the fortran source =20=

> to attempt a trace and it gets "lost" upon entering the gradient =20
> subroutine. This happens both for the largish 4600 atom file and for =20=

> a 158 atom file.
>
> The prm file in both cases is amber99.
>
>
> Thank you for any assistance,
>
> Ron Salesky
>
>
>
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