From owner-nwchem-users@emsl.pnl.gov Mon Apr 10 21:31:04 2006 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.6/8.13.6) with ESMTP id k3B4V37S013638 for ; Mon, 10 Apr 2006 21:31:03 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.6/8.13.6/Submit) id k3B4V3mq013637 for nwchem-users-outgoing-0915; Mon, 10 Apr 2006 21:31:03 -0700 (PDT) Date: Mon, 10 Apr 2006 21:31:01 -0700 From: "Valiev, Marat" Subject: RE: [NWCHEM] zcoord in QM/MM calculation To: JunJun Liu , nwchem-users@emsl.pnl.gov Message-id: <42C7E766869C42408F0360B7BF0CBD9B082A23@pnlmse27.pnl.gov> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-type: text/plain; charset=iso-8859-1 Thread-Topic: [NWCHEM] zcoord in QM/MM calculation thread-index: AcZdGrz9Fg+9hc3wR6i6YfQm7GOk1QAA3h5G Content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: References: X-OriginalArrivalTime: 11 Apr 2006 04:31:02.0028 (UTC) FILETIME=[BD24CCC0:01C65D20] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by odyssey.emsl.pnl.gov id k3B4V2xP013634 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Liu, QM/MM calculations do not use or work with geometry input block (in fact you should have never had one). As such none of the geometry directives (e.g. zcoord) are valid. Internally QM/MM does generate geometry object from the restart file. You can restrain a particular bond using constraints module (see user manual) provided you know the numbering of atoms (you can get that by, for example, running single point energy calculations). Best regards, ********************************************** * Marat Valiev * * Senior Research Scientist * * Molecular Sciences Software Group (NWChem) * * MSIN:K8-91 * * marat.valiev@pnl.gov * ********************************************** ________________________________ From: owner-nwchem-developers@emsl.pnl.gov on behalf of JunJun Liu Sent: Mon 4/10/2006 7:37 PM To: nwchem-users@emsl.pnl.gov Subject: [NWCHEM] zcoord in QM/MM calculation Hi all, I'm doing test on QM/MM calculation with the "zcoord" bond constraint. Since zcoord is a sub-directive of geometry, I input the cartesian coordinates of QM atoms under the geometry deck as follows: === geometry O -0.529 -0.222 -0.466 O -1.298 -2.366 -0.338 C -1.494 -1.186 -0.102 O -0.952 -1.015 1.501 H -1.627 -1.447 2.046 zcoord bond 3 4 2.0 constant end === The distance between atom 3 and atom4 in the geometry deck is 1.7 and I want to fix the distance to be 2.0 during the optimization. This distance was successfully changed to 2.0 before the QM/MM interface started. But after that, the distance was changed to 2.3 right after QM/MM interface started and began osillating, indicating that bonth new bond value and constraint do not work. Could anybody be so kine tell me what's the problem? Does zcoord(bond restraint) can be applied with QM/MM module? Best Regards! Liu -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China