From owner-nwchem-users@emsl.pnl.gov Sun Apr 9 18:46:53 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 k3A1krQ2024734 for ; Sun, 9 Apr 2006 18:46:53 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.6/8.13.6/Submit) id k3A1kr9N024733 for nwchem-users-outgoing-0915; Sun, 9 Apr 2006 18:46:53 -0700 (PDT) Date: Sun, 09 Apr 2006 21:46:47 -0300 From: JunJun Liu Subject: [NWCHEM] Bond constraint under QM/MM optimization To: "nwchem-users@emsl.pnl.gov" Message-id: MIME-version: 1.0 Content-type: text/plain; format=flowed; delsp=yes; charset=utf-8 Content-transfer-encoding: 8bit DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:date:to:subject:from:content-type:mime-version:content-transfer-encoding:message-id:user-agent; b=W0y7A88egXkbhGHntLDvwId2cxxuG6FJX2mVS7lwif8lVpHpLO+ceSGzzWxmz2T+e5Dw7ABO6YDUr6qs4FOn+JXCZEaPCq1ME47CWpV4bWzLACgW76EdDOEZbW6R+outO0RevnQNYple5nds9w44o0xSjZe0Fop2gjaeOIPCucI= User-Agent: Opera Mail/9.00 (Linux) Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Hi all, I want to do an optimization with a bond fixed under the QM/MM model. I did a test with "zcoord" to perform constraint on that bond. Here's my input: ====== Start ===== start ts1 echo memory 900 MB prepare system ts1_Re source prepare/1.pdb modify atom 1:_O1 quantum modify atom 1:_O2 quantum modify atom 1:_C8 quantum modify atom 1:_O5 quantum modify atom 1:_H1 quantum ignore update lists end task prepare md system ts1_Re sd 300 init 0.00001 min 1.0e-5 max 0.05 noshake solute memory 200000 end charge -1 dft iterations 100 end basis "ao basis" * library "6-31+G*" end driver maxiter 300 xyz test end geometry zcoord bond 3 4 1.7 r constant end end qmmm bq_exclude none link_atoms hydrogen optimization qm end task qmmm dft optimize ======= END ============== Then I got an error message complaining "too many centers", please see below for details ======= Start ======== User specification of redundant internal variables -------------------------------------------------- i j k l value name frz --- --- --- --- ------------ -------- --- 3 4 1.700000 r T Scaling coordinates for geometry "geometry" by 1.889725989 (inverse scale = 0.529177249) geom_cart_set: too many centers 0 geometry geom_masses_set: too many centers 0 geometry geom_nucexps_set: too many centers 0 geometry ------------------------------------------------------------------------ geom_input: geom_nucexps_set failed 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 46: end ======= END ========== I'm wondering if the bond constraint can be performed by "zcoord". If yes, could you please tell me how to do that? Thanks in advance! Regards! Liu -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China