From owner-nwchem-users Wed Sep 1 10:20:10 1999 Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.8.8+Sun/8.8.5) id KAA24443 for nwchem-users-outgoing; Wed, 1 Sep 1999 10:11:30 -0700 (PDT) Date: Wed, 01 Sep 1999 10:11:26 -0700 (PDT) From: TP Straatsma <d3j191@emsl.pnl.gov> Subject: Re: Periodic boundary conditions in MD In-reply-to: <3.0.5.32.19990901093743.00c422a0@poptart.llnl.gov> (message from Larry Fried on Wed, 01 Sep 1999 09:37:43 -0700) To: lfried@llnl.gov Cc: nwchem-users@emsl.pnl.gov Message-id: <199909011711.KAA11827@sounion.emsl.pnl.gov> Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk r> Date: Wed, 01 Sep 1999 09:37:43 -0700 r> From: Larry Fried <lfried@llnl.gov> r> Sender: owner-nwchem-developers@emsl.pnl.gov r> X-Sender: e294474@poptart.llnl.gov r> MIME-version: 1.0 r> X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) r> Content-type: text/plain; charset="us-ascii" r> Precedence: bulk r> r> Does anyone know how to specify periodic boundary conditions for NWARGOS r> for systems with no solvent ? Right now we are editing the .rst file by r> hand, but it would be nice if there were a cleaner way. r> r> Larry Fried r> Lawrence Livermore National Laboratory r> One way in which you could generate a periodic box without solvation is to increase the minimum solvent-solute distance to something larger than the periodic box size. For example: --- prepare system molecule_test solvate cube 0.5 touch 2.5 end task prepare --- should create a restart file for the molecule (for which the coordinates are read from a PDB file or geometry object) in the center of a periodic cubic box without any solvent. Another way would be: --- prepare system molecule_test periodic end task prepare --- but this would create a periodic rectangular box with dimensions that would just fit the molecule. This is probably not what you want in general. Hopefully this helps. -- T. P. Straatsma High Performance Computational Chemistry tel. +1 (509) 375-2802 Environmental Molecular Sciences Laboratory fax. +1 (509) 375-6631 Pacific Northwest National Laboratory e-mail: tp_straatsma@pnl.gov P.O.Box 999, MS K1-83, Richland, WA 99352 ------------------------------------------------------------------------------