From owner-chemistry@ccl.net Wed May 6 05:37:01 2009 From: "Mateusz Galuszka FQS Poland ccs[a]fqs.pl" To: CCL Subject: CCL: PHASE software Message-Id: <-39238-090506052959-8665-NDzRbiU7D4lrrX9PUFvgUA a server.ccl.net> X-Original-From: "Mateusz Galuszka [FQS Poland]" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 06 May 2009 10:29:37 +0200 MIME-Version: 1.0 Sent to CCL by: "Mateusz Galuszka [FQS Poland]" [ccs]^[fqs.pl] Dear Jonas, The PHASE software has been recently integrated with Fujitsu SCIGRESS (new version of Fujitsu CAChe/Scigress Explorer) software. SCIGRESS contains interface to most of the PHASE capabilities, and English manual and tutorial (a few simple examples). Of course all tasks including creating input, running jobs and viewing results can be accomplished from SCIGRESS environment. PHASE is a free code (as well as its GUI) but there are no informations/manuals/tutorials for the standalone version. The only access for non Japanese-speaking researchers is currently through SCIGRESS software. If you would like to receive some more information on PHASE (manual, free trial etc), please contact me directly. Best regards, Mateusz -- Mateusz Galuszka Sales & Marketing Specialist FQS Poland, FUJITSU Group ul. Parkowa 11, 30-538 Krakow, Poland Tel: (+48) 12 429 43 45 Fax: (+48) 12 429 61 24 Mobile: (+48) 666 010 305 E-mail: ccs:fqs.pl; m.galuszka:fqs.pl http://www.fqs.pl Jonas Baltrusaitis jonas-baltrusaitis~~uiowa.edu wrote: > Sent to CCL by: "Jonas Baltrusaitis" [jonas-baltrusaitis^-^uiowa.edu] > Dear all, > > is anybody familiar with PHASE, a solid state software package created by a research group at National Inst. for Materials Science in Japan (Mr. Takahisa OHNO, project leader). > > It's an outstanding package and has an ultimate input creator/viewer/submitter. The biggest problem: no English manual and/or support forum (at least not that I know of). > > So I was wondering if anybody could share some light on that software and if an English manual can be retrieved or point of contact/mailing list/user forum > > thanks > > Jonas Baltrusaitis > University of Iowa> > > > > From owner-chemistry@ccl.net Wed May 6 09:45:01 2009 From: "Jim Kress ccl_nospam:-:kressworks.com" To: CCL Subject: CCL:G: QM/MM and copper Message-Id: <-39239-090505201640-16257-Zay2eQ5fXC72GWGpVUTeMA!A!server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 5 May 2009 19:56:41 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam.^-^.kressworks.com] There are a plethora of computer programs which will perform the task of interest to you. They are (in no particular order): GAMESS http://www.msg.ameslab.gov/GAMESS/ NWCHEM http://www.emsl.pnl.gov/docs/nwchem/nwchem.html FireFly http://classic.chem.msu.su/gran/gamess/index.html CPMD/gromacs http://www.cpmd.org/ http://www.gromacs.org/ Quantum ESPRESSO http://www.quantum-espresso.org/ Will do what you want without resorting to a QM/MM approach, as will CP2K http://cp2k.berlios.de/ This list is not meant to be exhaustive, in-as-much-as I am sure there are many other codes that will work for you. Good luck. Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com^-^ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com^-^ccl.net] > On Behalf Of Gustavo Seabra gustavo.seabra*o*gmail.com > Sent: Tuesday, May 05, 2009 1:13 PM > To: Kress, Jim > Subject: CCL:G: QM/MM and copper > > > Sent to CCL by: Gustavo Seabra [gustavo.seabra~~gmail.com] On > Mon, May 4, 2009 at 6:26 PM, Syed Tarique Moin > tarisyed^_^yahoo.com wrote: > > > > Sent to CCL by: "Syed Tarique Moin" [tarisyed-$-yahoo.com] Dear CCl > > users, > > > > I am trying to simulate the copper containing > metalloprotein. For the QM/MM, i am using the hybrid software > method incorporating Gaussian as the QM source and Amber as a > MM using pupil package interface. Can anybody tell me free > package other than pupil for interfacing these two programs > and the good basis set for the copper (II) coordinated with > amino acids. > > > > Regards > > Hi Syed, > > I'm not sure there is another free program to do what you > want. Is there a specific reason you can't use PUPIL for it? > > Gustavo. > > > > -=his is automatically added to each message by the mailing > script = To recover the email address of the author of the > message, please change the strange characters on the top line > to the ^-^ sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Wed May 6 10:43:01 2009 From: "Vincent.Leroux{}loria.fr" To: CCL Subject: CCL: docking Message-Id: <-39240-090506101607-28163-Oydb0dV5YFFDWwXl18D+MA ~ server.ccl.net> X-Original-From: Vincent.Leroux!=!loria.fr Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 06 May 2009 16:15:55 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent.Leroux\a/loria.fr Hello, No need to SHOUT OUT LOUD... GOLD, Glide and ICM-Docking are fine docking packages. You can also =20 use DOCK or AutoDock if your institution cannot afford them. I would recommend NAMD for MD simulations. VL "neeraj misra neerajmisra!=3D!hotmail.com" a =E9cr= it=A0: > > Sent to CCL by: "neeraj misra" [neerajmisra[-]hotmail.com] > PLEASE SUGGEST SOME GOOD PACKAGE FOR DOCKING STUDIES AND MD SIMULATION. > > From owner-chemistry@ccl.net Wed May 6 13:21:01 2009 From: "Richard Leo Wood woodx278%%umn.edu" To: CCL Subject: CCL: docking Message-Id: <-39241-090506122202-15673-qW3gB2xiEjHPIMjQ8YLRRg(~)server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Wed, 6 May 2009 12:21:58 -0400 Sent to CCL by: "Richard Leo Wood" [woodx278() umn.edu] Hi all, I would add Surflex-Dock to the list of docking programs, unlesss you need to do flexible receptor or constrained docking. If you're doing protein MD, I would recommend CHARMm. Cheers, Richard Sent to CCL by: Vincent.Leroux\a/loria.fr Hello, No need to SHOUT OUT LOUD... GOLD, Glide and ICM-Docking are fine docking packages. You can also use DOCK or AutoDock if your institution cannot afford them. I would recommend NAMD for MD simulations. VL From owner-chemistry@ccl.net Wed May 6 17:04:01 2009 From: "Keith Refson krefson ~ googlemail.com" To: CCL Subject: CCL: One unpaired electron - Zero integrated spin density? Message-Id: <-39242-090506140517-25354-htjth6KDOE13Obn5B+J3vg^server.ccl.net> X-Original-From: Keith Refson Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 06 May 2009 17:49:12 +0100 Mime-Version: 1.0 Sent to CCL by: Keith Refson [krefson^^googlemail.com] Dear Dr Garrison, On Fri, 2009-05-01 at 07:44 -0400, Stephen.Garrison]=[srnl.doe.gov wrote: > > Could someone explain to me how a system can have one unpaired > electron, but nearly zero integrated spin density? > > I am using CASTEP (LDA functional) and am working on a periodic > metallic system with 189 electrons. > [snip] > 2*Integrated Spin Density = -0.337735E-03 > 2*Integrated |Spin Density| = 0.612583E-02 > > This does not make much physical sense to me. How can a system have an > unpaired electron but zero integrated absolute value(spin density)? > What am I missing? You don't have 189 electrons, you have an infinite number of electrons, half of which are spin-up and half spin-down. This is the physics that a periodic solid-state code is attempting to model. More specifically, the infinite number of electrons is represented as Bloch functions with two state indices band m and wavevector k. This transforms the model system from an inconveniently large infinite one with orbitals extending over all space to a finite one with orbitals represented only within a finite periodic simulation cell. The integration over all occupied states transforms into an integral over wavevector k which is further approximated using a discrete grid of k-points. If a band does not cross the Fermi level it must contain 0, 1, (or 2 for non-spin polarized calculations) "electrons" *per cell* as it is entirely occupied or unoccupied. In the case of a metallic system the number of "electrons" per cell in a band need not be an integer if that band crosses the Fermi level. In "real" physics terms this simply means that some fraction of the infinite number of electronic states is occupied. And a nonmagnetic system is one in which the selfconsistent potential results in equal numbers of spin up and spin down. This was not really a CASTEP specific question, and could apply to any periodic QM code, but if you have any there is a CASTEP email list which you can join at https://www.jiscmail.ac.uk/castep. This is mostly an "academic" list, and not for questions about the commercial Accelrys GUI, but otherwise users of the commercial product are also welcome. sincerely Keith Refson -- Dr Keith Refson, Building R3 Rutherford Appleton Laboratory Chilton Didcot Oxfordshire OX11 0QX T: 01235 778023 Keith.Refson#%# F: 01235 445720 #%#stfc.ac.uk