From chemistry-request@ccl.net Mon Nov 25 10:18:50 1991 Date: Mon, 25 Nov 91 10:07:57 EST From: G. Ravishanker To: chemistry@ccl.net Subject: BIOGROMOS Status: R Hi I am interested to hear from anyone who knows anything about BIOGROMOS, apparently a graphical front-end to GROMOS. Thanks in advance. Ravi From chemistry-request@ccl.net Mon Nov 25 12:14:10 1991 From: Karthik Iyer Date: Mon, 25 Nov 91 09:46:29 -0500 To: chemistry@ccl.net Subject: Any software for Normal Mode Analysis? Status: R Dear fellow netters, I would be interested in finding out if there is any public domain or share-ware software that does normal mode analysis. More specifically, I am looking for software that does 1. factor group analysis and 2. identification of normal modes as belonging to any particular Irr. Rep. . Any help would be appreciated and thank you in advance. Karthik Iyer iyer@sodium.mps.ohio-state.edu From chemistry-request@ccl.net Mon Nov 25 14:25:56 1991 From: Karthik Iyer Date: Mon, 25 Nov 91 13:54:26 -0500 To: chemistry@ccl.net Subject: Re : software for Normal Mode Analysis Status: R >Dear fellow netters, > I would be interested in finding out if there is any public >domain or share-ware software that does normal mode analysis. More specifically, >I am looking for software that does > 1. factor group analysis > and 2. identification of normal modes as belonging to any particular Irr. >Rep. . >Any help would be appreciated and thank you in advance. > >Karthik Iyer >iyer@sodium.mps.ohio-state.edu I am sorry that I did not make myself clear in that I wanted information on NMA of crystal systems. Karthik Iyer iyer@sodium.mps.ohio-state.edu From chemistry-request@ccl.net Mon Nov 25 14:52:26 1991 Date: Mon, 25 Nov 91 14:20:48 EST From: Mark Murcko To: chemistry@ccl.net Subject: DEC versus HP versus IBM ... Status: R First of all, thanks to everyone who responded to my request last week for information about HP versus IBM. There are obviously some differences of opinion depending on what kinds of code you look at, but overall the picture is fairly clear for molecular dynamics-type simulations. Now for the next request. Several people who responded went out of their way to mention that DEC is soon going to announce something competitive. Although I remain skeptical, I have now heard quite a lot about the "alpha" chipset and some other, deeper, darker, secrets brewing at the Mill. So, does anyone know anything more concrete about what DEC is doing? Is there any chance that they could come out with a real product in the HP730 - IBM550 class anytime soon? Any (new) information appreciated! / Mark (markm@vpharm.com) From chemistry-request@ccl.net Mon Nov 25 15:20:03 1991 Date: Mon, 25 Nov 1991 14:05 CDT From: MEDCHEM@LIFE.UAMS.EDU Subject: stereo adapters To: chemistry@ccl.net Status: R Does anybody knows the source of stero adapters for silicon graphics? Thanks. J. Smith medchem@uams.bitnet From chemistry-request@ccl.net Mon Nov 25 16:25:23 1991 Date: Mon, 25 Nov 91 22:08:47 +0100 From: martin@link.sunet.se (Martin Norin, Dept. Biochem., Royal Inst. Technol., Stockholm, tel. +46-8-7907512, e-mail; martin@physchem.kth.se) To: "chemistry@ccl.net"@kth.sunet.se Subject: reply:BIOGROMOS Status: R Hi Ravi, BIOGROMOS is a graphical and user friendly front end to GROMOS. It contains a lot of graphical analysis tools for dynamic runs and also builders for biomolecules and small molecules. The program is commercial and sold by BIOSTRUCTURE, Strasbourgh, France. BIOSTRUCTURE have announced that the program is going to include MM2 and AMBER engines in the near future. To my knowledge BIOGROMOS runs on both Silicon Graphic (not on the INDIGO) and ESV workstations. However I belive that it is optimized for several other platforms that I'm not aware of (IBM, DEC etc). We have just purchased a copy of the program for our ESV machine. The tape arrived last week and I haven't got time to explore the program yet, but adress me directly and I will give you more information and a contact to the BIOSTRUCTURE people if you want. Greetings, /martin --------------------------------------------------------------------------- Martin Norin tel: +46-8-7907512 Dept.Biochem. fax: +46-8-7231890 Royal Inst. Technol. e-mail(bitnet): martin@physchem.kth.se 100 44 Stockholm Sweden --------------------------------------------------------------------------- From chemistry-request@ccl.net Mon Nov 25 17:03:11 1991 Date: Tue, 26 Nov 1991 08:40:49 +1100 From: apa@ccadfa.cc.adfa.oz.au (Alan P Arnold) To: chemistry@ccl.net Subject: Radial Distribution Functions from MD simulations Status: R Dear colleagues, before I embark on wheel-reinvention, I would like to hear from anyone who has calculated radial distribution functions from coordinate data obtained during a MD simulation. I am particularly interested in hearing from Biosym InsightII/ Discover or Amber users who have done this and are willing to share their expertise and more importantly, their code! The main concern at the moment is to calculate and visualise g(r) for Zn-O interactions of a zinc(II) cation in a box of waters. Can InsightII's 'plot-a-function' or 'plot-a-function-from-a-file' procedures be used to *calculate* g(r) and subsequently plot it?? Any comments are welcome, thanks for listening ---- Dr Alan Arnold | Phone: +61 62 68 8080 Chem. Department,University College | ACSNET: apa@ccadfa.cc.adfa.oz.au Australian Defence Force Academy | UUCP: ...!seismo!munnari!ccadfa.oz!lpb CANBERRA ACT 2600 Australia | ARPA: apa%ccadfa.oz@SEISMO.CSS.GOV