From owner-chemistry@ccl.net Thu Jul 13 08:11:00 2006 From: "Jens Thomas j.m.h.thomas(-)dl.ac.uk" To: CCL Subject: CCL: Freezing angles in GAMESS-UK/CHARMM QM/MM simulations? Message-Id: <-32120-060713075128-30071-DJo1GWZe79Xwe0xyo9VyTQ++server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Jul 2006 12:14:43 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas .. dl.ac.uk] Dear James, It is possible to hold an angle or bond length constant in GAMESS-UK, provided that the molecule has been defined with a Z-matrix. If this is the case, then you can decide which of the bond lengths and angles are free to vary and those that are to be held constant. There is more information on this in the GAMESS-UK manual at: http://www.cfs.dl.ac.uk/docs/gamess_manual/chap3/node11.html If you don't have a Z-matrix definition for your molecule, than the freely available CCP1GUI has the ability to automatically construct a Z-matrix definition from Cartesian coordinates. You can find out more about the CCP1GUI at: http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml Whether this is possible for QM/MM modelling depends on the QM/MM environment within which you are using GAMESS-UK. If that permits the QM region to be defined with a Z-matrix, or supports constraining certain bonds and angles itself, there should be no problem in keeping the relevant bonds and angles fixed. I hope this helps. Best wishes, Jens James N Scott scottjn],[gmail.com wrote: > Sent to CCL by: "James N Scott" [scottjn-$-gmail.com] > Greetings CCLers. I am on the verge of purchasing GAMESS-UK in order to do some simple QM/MM simulations of different small molecules in water, with the goal of examining solvent effects on spectra. > > Is it possible to make constant an angle or bond length internal to the QM system of interest? For instance, can I fix a dihedral angle between two QM molecules embedded in MM water molecules, or a bond length within a single QM molecule? > > Thanks very much for any assistance! > > J. Nathan Scott> > > > > >