[MMTK] Fwd: Question about OrthorhombicPeriodicUniverse

Konrad Hinsen research at khinsen.fastmail.net
Sat Feb 9 08:38:51 UTC 2013

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From: mmtk-bounces at starship.python.net
To: mmtk-owner at starship.python.net
Subject: Auto-discard notification
Date: Fri, 08 Feb 2013 22:26:51 +0000

The attached message has been automatically discarded.
From: "Houtman, Carl -FS" <choutman at fs.fed.us>
To: "mmtk at starship.python.net" <mmtk at starship.python.net>
Subject: Question about OrthorhombicPeriodicUniverse
Date: Fri, 8 Feb 2013 21:40:45 +0000

I’m running MMTK on a Win32 platform with Python 2.7.3.  I was just trying to build a
periodic box of water. I can build the array of water just fine, and run a small dynamic
simulation, if I use “InfiniteUniverse”.  Now when I try to run a
“OrthorhombicPeriodicUniverse” the energy evaluation seems to go crazy.  An example of
the output is

Temperature:  108.995945042

Momentum:  [-8.99110369177641, 9.860928206426244, 17.34781808242614]

Angular momentum:  [-12.017048928234056, 18.469094173984196, -9.2804957707983]

Step 0

Time: 0.000000

Potential energy: -1.#IND00, Kinetic energy: 81.561925

Step 10

Time: 0.010000

Potential energy: 1.#QNAN0, Kinetic energy: 1.#QNAN0

The universe definition is

universe = OrthorhombicPeriodicUniverse((2*Units.nm, 2*Units.nm, 2*Units.nm), \

                   Amber99ForceField(1.0*Units.nm, mod_files=['frcmod.ff99SB']))

Any ideas?  I don’t get any raised errors it just continues giving NAN after NAN



Carl Houtman PhD <choutman at fs.fed.us>
Research Chemical Engineer
USDA, Forest Service, Forest Products Lab
One Gifford Pinchot Drive
Madison, WI 53726
(608) 231-9445
(608) 231-9538 (FAX)

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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net

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