From owner-chemistry@ccl.net Fri Apr 23 12:14:00 2010
From: "Jim Kress ccl_nospam^^kressworks.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: TINKER sovation with polar molecules
Message-Id: <-41708-100423113946-4989-7WkurxNLOk0pQmSFRb52Yg##server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam+*+kressworks.com>
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Date: Fri, 23 Apr 2010 11:39:29 -0400
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Sent to CCL by: "Jim Kress" [ccl_nospam- -kressworks.com]
Try gromacs

http://www.gromacs.org/

For MD it is faster than Tinker, easier to use, runs in parallel, and
supports just as many classical force fields - along with a variety of
multiple time scale (and other) methods not available in Tinker.  It also
provides a much larger set of tools to analyze and interpret your results.

The same could be said for LAMMPS

http://lammps.sandia.gov/

with the additional comment that classical AND REACTIVE force fields are
also supported (e.g. REAXFF).

Jim

> -----Original Message-----
> From: owner-chemistry+ccl_nospam==kressworks.com . ccl.net [mailto:owner-
> chemistry+ccl_nospam==kressworks.com . ccl.net] On Behalf Of Kelly 8D
> i.m.smilin.kelly]_[gmail.com
> Sent: Thursday, April 22, 2010 2:09 PM
> To: Kress, Jim 
> Subject: CCL: TINKER sovation with polar molecules
> 
> Hi CCL users!
> 
> I am trying to solvate a small molecule in water using TINKER.  I have
searched the
> archives, and found references to xyzedit and soak.  I don't have soak, so
am using
> xyzedit.
> 
> When generating the water with xyzedit (option 16), the water box contains
water
> molecules that are all aligned in the same direction.  So when I try to
minimize,
> optimize, or Newton the xyz file, to relax it into something i can do MD
on, the
> program crashes with:
> 
> 
> INDUCE   --   Warning, Induced Dipoles are not Converged
> 
> TINKER is Unable to Continue; Terminating the Current Calculation
> 
> 
> I find that small systems (~<30 waters) will run - probably because the
system as a
> whole has less dipole moment - but I know most users are making bigger
boxes
> than that...
> 
> How are you relaxing the system enough to do MD?
> 
> 
> If you prefer to reply in person, e-mail is kelly.theel=email.ucr.edu
> 
> Thanks for any help you can give!
> 
> --
> - Kelly
> 
> "Most folks are about as happy as they make up their minds to be."  -
Abraham
> Lincoln