From chemistry-request@server.ccl.net Sat Oct 21 07:11:45 2000 Received: from dsmtp16.dion.ne.jp (dsmtp16.dion.ne.jp [211.5.1.117]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA15617 for ; Sat, 21 Oct 2000 07:11:44 -0400 Received: from b159504364 by dsmtp16.dion.ne.jp (8.9.3/3.7W-00061517) id UAA06308; Sat, 21 Oct 2000 20:11:31 +0900 (JST) Message-ID: <004501c03b4f$754b53e0$1123fbd2@b159504364> From: "Telkuni" To: Subject: Free MD program for Win95/98 --SUMMARY Date: Sat, 21 Oct 2000 20:09:57 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi ! all CCLers, Several days ago, I wrote: >I am a novice of MD simulation. >I'm looking for "free" and "for non-Bio" MD programs which are able >to run on Win95/98. >If anyone know such MD programs(and I wish they are also easy to use >for beginners.) , please teach me. >I would like to use them for "MD-learning". Soon, there were many responses. I summarize them. Overviewing them, "TINKER" is very famous and suitable for my purporse. Thanks a lot ! ----- 1)from Laurence Cuffe --------------- Do a web search for "tinker" its free and it seemed quite easy to get started with when I played with it. Laurence Cuffe ----- 2)from David van der Spoel --------------- GROMACS will run on windows PCs, but not with a windows interface. You need the GNU compilers for windows. http://md.chem.rug.nl/~gmx ----He also said: It is not specific for biomolecules, it does everything. The only problem is that you have to find a force field for the molecule you want to study and build a topology. ----- 3)from Andreas Goeller --------------- Hi, try tinker. http://dasher.wustl.edu/tinker/ -- Andreas Goeller ----- 4)from Eric Dehaudt -------------- Hi, I use a software called DLPOLY for MD calculations. It's free and available on the net on the CPP5 site (research group of great britain). It has been developed by Williams Smith and al, of the University of Daresbury, for SUN, CRAY, Silicon graphics, and other plateform but not for PC's. However, it's easy to compile it for Windows NT ( or 98), what I have done. I work today on PC plateform. The software is quite easy to use but have no graphical interface. To visualise I advice you to use VMD software (release 1.6a), free of charge too and available on the net on the VMD site (see message on CCL liste last week). You will have to convert input and output files (see the BABEL software to convert, free too : it won't be enough but it can help). That the configuration I use up to now. If you find better, please, let me know. Feel free to contact me for further questions. Best regards. Eric Dehaudt Ecole des Mines de Paris Sophia Antipolis, France ----- 5)from Mateusz Nowak --------------- Hi. 3 programs come to my mind: 1. Tinker (DOS binaries downoadable from home page http://dasher.wustl.edu/tinker/). 2. AMMP http://asterix.jci.tju.edu/ammp.html (entirely for Win) 3. Gromacs http://rugmd0.chem.rug.nl/~gmx/ is distributed as source code, but has standard makefile for Cygwin (Unix emulator for Win 9x/NT), and compiles without problems. Many others you can find at http://sal.kachinatech.com/Z/2/index.shtml Goodluck. Mateusz ---- He also said: Indeed, Gromacs is intended rather for biomolecular simulations (proteins, nucleic acids & lipid bilayers). It contains parameters of Gromos87 and Gromos96 force fields. As far as I remember you wanted something for smaller compounds (organic?). The Tinker package (I guess) contains parameter sets of Amber (and others) force fields, which can be suitable for your purposes. But you have to check it, I myself perform simulations of proteins and not sure, which force field will work in case of small compounds. I think there's another program, called MOIL (from Cornell Univ.), which runs under Win, even has GUI. But again, it's more for biomolecules. Regards Mateusz ----- 6)from Andre Mauricio de Oliveira --------------- Dear Telkuni, Try TINKER (http://dasher.wustl.edu/tinker/). Greets. ***************************************** Telkuni telmail@d4.dion.ne.jp *****************************************