From noy@tci005.uibk.ac.at Thu Oct 27 09:21:23 1994 Received: from uibk.ac.at for noy@tci005.uibk.ac.at by www.ccl.net (8.6.9/930601.1506) id JAA27031; Thu, 27 Oct 1994 09:01:58 -0400 Received: from tci005.uibk.ac.at by uibk.ac.at with SMTP id AA09393 (5.65c/IDA-1.4.4 for ); Thu, 27 Oct 1994 14:00:48 +0100 Received: by tci005.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA32112; Thu, 27 Oct 1994 14:00:49 +0100 From: noy@tci005.uibk.ac.at (Noy) Message-Id: <9410271300.AA32112@tci005.uibk.ac.at> Subject: 100% parallel algorithm in MD To: chemistry@ccl.net Date: Thu, 27 Oct 1994 14:00:49 +0100 (NFT) Cc: krl@tci005.uibk.ac.at (Klaus R. Liedl, phone 507/5164), bmr@tci001.uibk.ac.at, ypp@tci002.uibk.ac.at, supot@atc.atccu.chula.ac.th, krisana@sura1.sut.ac.th X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 2051 Dear cyberchemists, From the principle of molecular dynamics, velocity is reversible. Thus, if we assign a minus sign to all velocity of every particle in the simulation box ( at any equilibrated state ), the trajectory should be recoverd to the past correctly. This is not a new idea but I wonder if somebody has practiced it. For example if we simulate the phase space at time orgin t0 to the time t1, t0 ----------------> t1 (1 picosecond) Then, we revert velocity of all particles of the configuration at the time t0. Simulates it back to the past to the time t2 t0 ----------------> t2 (1 picosecond) Then we have the past trajectory. If we connect the two trajectories together, we will have t2 -------------------> t0 -----------------> t1 (2 picoseconds) Thus, we must revert the sign of velocity of the configurations from the time t1 to the time t0. We will have the overall longer trajectory of the simulation. Given the run of two trajectories running in parallel on two computers, one can save time by the factor of 2. The dynamics and structural properties should be calculated from the time origin t2 to the time t1. Does somebody have comments or suggestions on this ? Is it correct ? If this idea is practical, it would help to save time a lot. Imagine if I have to run MD for 10 ps to evaluate diffusion coefficient more precisely, I can divide the work into 2 jobs. One job is simulated on a computer. For another job, I convert the velocity and trace the phase space back to it past, have it run on another computer parallelly. Connect two jobs together by going back to the origin of the phase space in the far past time. Evaluate the time evolution and then I should get the results much faster. After all, the parallel efficiency is 100 % !!!!!!!! Thanks for your comments. best wishes, Teerakiat From given@tiber.nist.gov Thu Oct 27 12:21:31 1994 Received: from tiber.nist.gov for given@tiber.nist.gov by www.ccl.net (8.6.9/930601.1506) id LAA29582; Thu, 27 Oct 1994 11:30:51 -0400 Received: by tiber.nist.gov (5.64/10.1) id AA05066; Thu, 27 Oct 94 11:31:52 -0400 Date: Thu, 27 Oct 94 11:31:52 -0400 From: given@tiber.nist.gov (James A Given) Message-Id: <9410271531.AA05066@tiber.nist.gov> To: CHEMISTRY@ccl.net, frank@caesar.wustl.edu Subject: Re: CCL:codes for Ising model You better connect the spins on each edge to spins on the opposite edge (i.e. use toroidal boundary conditions) or the results probably will be misleading. From tore@physchem.kth.se Thu Oct 27 12:32:30 1994 Received: from link.physchem.kth.se for tore@physchem.kth.se by www.ccl.net (8.6.9/930601.1506) id MAA00560; Thu, 27 Oct 1994 12:16:00 -0400 From: Received: by physchem.kth.se (MX V4.0-1 VAX) id 3; Thu, 27 Oct 1994 17:16:15 EDT Date: Thu, 27 Oct 1994 17:16:14 EDT To: chemistry@ccl.net Message-ID: <00986946.E9672D20.3@physchem.kth.se> Subject: Parameters for Dummy atoms I need MM3 parameters for trigonal Cu(I). In our model system the cu atom is bonded to ethylene. Due to the low rotational barrier for the Cu-ethylene bond I beleive it is necessary to describe this bond using a dummy atom. However, we have not been able to figure out how to do the parameterization for the dummy atom. I am therefore interested in references to earlier work dealing with the parameterization of dummy atoms. Any hint or suggestion on how to solve this problem would also be appreciated. In general, is there any program or algorithm developed for parameterization with ab initio energies as input, and is this program/algorithm dealing with Dummy atoms? Fredrik Haeffner Organic Chemistry Royal Institute of Technology Stockholm fredh@orgchem.kth.se From DTCCM@jazz.ucc.uno.edu Thu Oct 27 13:21:38 1994 Received: from jazz.ucc.uno.edu for DTCCM@jazz.ucc.uno.edu by www.ccl.net (8.6.9/930601.1506) id MAA01379; Thu, 27 Oct 1994 12:56:47 -0400 From: Received: from jazz.ucc.uno.edu by jazz.ucc.uno.edu (PMDF #2820 ) id <01HIRNMSLE8G8XBX24@jazz.ucc.uno.edu>; Thu, 27 Oct 1994 10:34:01 CST Date: 27 Oct 1994 10:34:01 -0600 (CST) Subject: MOPAC for SGI Personal Iris v 4.0 To: chemistry@ccl.net Message-id: <01HIRNMSLNVM8XBX24@jazz.ucc.uno.edu> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, Does anyone know where I can locate a copy of compiled MOPAC for the Silicon Graphics Personal Iris ver. 4.0. We have attempted to compile the source code to no avail. Thank you, Don Coupe University of New Orleans dtccm@jazz.ucc.uno.edu From sling@euclid.chem.washington.edu Thu Oct 27 14:21:29 1994 Received: from euclid.chem.washington.edu for sling@euclid.chem.washington.edu by www.ccl.net (8.6.9/930601.1506) id OAA05062; Thu, 27 Oct 1994 14:08:57 -0400 Received: by euclid.chem.washington.edu (AIX 3.2/UCB 5.64/4.03) id AA39934; Thu, 27 Oct 1994 11:07:49 -0700 Date: Thu, 27 Oct 1994 11:07:49 -0700 From: sling@euclid.chem.washington.edu (Song Ling) Message-Id: <9410271807.AA39934@euclid.chem.washington.edu> To: chemistry@ccl.net, noy@tci005.uibk.ac.at Subject: Re: CCL:100% parallel algorithm in MD Cc: bmr@tci001.uibk.ac.at, krisana@sura1.sut.ac.th, krl@tci005.uibk.ac.at, sling@euclid.chem.washington.edu, supot@atc.atccu.chula.ac.th, ypp@tci002.uibk.ac.at You proposed that by reversing all momenta (velocities when they are proportional to momenta) you can connect two pieces of integrated trajectories together to form a longer one, unfortunately this is incorrect in general. Here is a simple example, the trajectory of a harmonic oscillator in phase space is a closed topological circle, and for an initial condition (x,p) in the first quadron (spell), when you reverse its momentum (velocity), you will end up in the 4th quadron, integrating the trajectory for a time dt, your first trajectory is still in the first quadron, while your another trajectory is still in the 4th quadron, the two pieces simply don't connect. The problem originated from that you didn't think about the trajectories as phase space objects (flows), you had a coordinate space picture. It is indeed possible to connect two pieces of trajectories to form a longer one in phase space, the way to do it is to integrate backward in time for -dt, and then integrate forward in time for dt, endding up a trajectory of "length" 2dt. Do not reverse the signs of the momenta (velocities) of your initial point. (You stay at the same point in phase space.) But this approach may be error prone depending on how many time steps you integrate your trajectory, if your system is very sensitive to initial conditions, the chances are after you integrate a trajectory from point A to point B, your integrate backward from B (with -dt) you may not end up in A. You seemed to be a little confused with the concept of "time reversal symmetry", to be safe let's say you have a conservative system (non- dissipative), the total energy is a constant of the motion, time reversal symmetry says that looking at the trajectories in phase space you don't find the arrow of time. In the harmonic oscillator example above, you have a topological circel in the phase space, you can parameterize it such that a point on it runs counterclockwise or clockwise, corresponding to running time forward or backward. If you have a damped harmonic oscillator, your trajectory spirals into the origin, the fixed point, now you have an arrow of time, past is mapped into the future. In short, you do not apply time reversal to join two pieces of trajectories together; you integrate forward and backward in time to do that. I don't know if that will save you computer time. From glee@chem0sun.calstatela.edu Thu Oct 27 16:23:00 1994 Received: from eagle.calstatela.edu for glee@chem0sun.calstatela.edu by www.ccl.net (8.6.9/930601.1506) id PAA06589; Thu, 27 Oct 1994 15:23:54 -0400 Received: from neptune.calstatela.edu by eagle.calstatela.edu with SMTP id AA06760 (5.65c/IDA-1.4.4 for ); Thu, 27 Oct 1994 12:22:54 -0700 Received: from chem0sun.calstatela.edu by neptune.calstatela.edu (4.1/SMI-4.1) id AA18190; Thu, 27 Oct 94 12:20:44 PDT Received: by chem0sun.calstatela.edu (4.1/SMI-4.1) id AA01611; Thu, 27 Oct 94 12:19:25 PDT Date: Thu, 27 Oct 94 12:19:25 PDT From: glee@chem0sun.calstatela.edu (Ging Lee 12-06-90) Message-Id: <9410271919.AA01611@chem0sun.calstatela.edu> To: chemistry@ccl.net Subject: PDB reader for Mac? Dear netters, I would like to know what are the names of some of the molecular modelling programs for a Mac to read pdb files. I recalled seeing some, but have since forgotten the name. I would help if it was a public domain program too. I am trying to make slides for an organic chemist for his protein structure class. Thank you very much in advance. Nicholas Lee glee@chem0sun.calstatela.edu From h.rzepa@ic.ac.uk Thu Oct 27 17:21:33 1994 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id QAA07772; Thu, 27 Oct 1994 16:40:01 -0400 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Thu, 27 Oct 1994 20:39:54 +0000 Received: from anxa02 by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA22620; Thu, 27 Oct 94 20:39:48 GMT X-Sender: rzepa@129.31.80.14 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 27 Oct 1994 21:45:16 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa, Henry) Subject: Scientific and Chemical Fonts Does anyone know of any ISO standard 8-bit (or even 16 bit!) character sets useful to chemists? I am aware of one Truetype chemistry font deposited at OSC, but is it "standard"? I ask because at the WWW conference at Chicago, a plea went out for good quality scientific fonts for use with WWW browsers, ie the font must be capable of inclusion on X11 R7 as well as PC and Mac systems. There is currently an IETF working party meeting in December to finalise the issue of how character sets other than the ISO Latin-1 can be defined in e.g. WWW browsers. This is the ONLY character set currently supported in HTML, and is pretty limited. A scientific character set implemented in PS, Truetype and bitmap fonts for X11and personal computers in the public domain would be precious to us all. Also for information is the implication that HTML 2.1 will support additional fonts, although it may be some time before WWW browsers implement the HTML 2.1 dtd. Dr Henry Rzepa, Dept. Chemistry, Imperial College, London, SW7 2AY. Tel: +44 171 594 5809. Fax: +44 171 594 5804. E-mail: rzepa@ic.ac.uk http://www.ch.ic.ac.uk/rzepa.html. Sent via MacPPP/MacTCP using Eudora 2.1 From sunger@crl.com Thu Oct 27 18:21:30 1994 Received: from mail.crl.com for sunger@crl.com by www.ccl.net (8.6.9/930601.1506) id RAA08493; Thu, 27 Oct 1994 17:23:27 -0400 Received: from crl8.crl.com by mail.crl.com with SMTP id AA02503 (5.65c/IDA-1.5 for ); Thu, 27 Oct 1994 14:23:12 -0700 Received: by crl8.crl.com id AA13661 (5.65c/IDA-1.5); Thu, 27 Oct 1994 14:23:05 -0700 Date: Thu, 27 Oct 1994 14:23:04 -0700 (PDT) From: Stefan Unger To: Ging Lee 12-06-90 Cc: chemistry@ccl.net Subject: Re: CCL:PDB reader for Mac? In-Reply-To: <9410271919.AA01611@chem0sun.calstatela.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try the new Protein Expert. Commercial package with steep introductory discount and very low academic pricing, especially for students. Check it out on www.camsci.com BioSoftware Marketing 415-858-0522 On Thu, 27 Oct 1994, Ging Lee 12-06-90 wrote: > > Dear netters, > > I would like to know what are the names of some of the molecular > modelling programs for a Mac to read pdb files. I recalled seeing some, > but have since forgotten the name. I would help if it was a public > domain program too. I am trying to make slides for an organic chemist for > his protein structure class. > > Thank you very much in advance. > > Nicholas Lee > glee@chem0sun.calstatela.edu > > ---Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > > From hinsenk@ERE.UMontreal.CA Thu Oct 27 19:21:30 1994 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id SAA10826; Thu, 27 Oct 1994 18:33:15 -0400 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA01735 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Thu, 27 Oct 1994 18:31:05 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA16241; Thu, 27 Oct 94 18:31:04 -0400 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA26919; Thu, 27 Oct 94 18:31:04 -0400 Date: Thu, 27 Oct 94 18:31:04 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9410272231.AA26919@cyclone.ERE.UMontreal.CA> To: h.rzepa@ic.ac.uk Cc: CHEMISTRY@ccl.net In-Reply-To: (h.rzepa@ic.ac.uk) Subject: Re: CCL:Scientific and Chemical Fonts Does anyone know of any ISO standard 8-bit (or even 16 bit!) character sets useful to chemists? I am aware of one Truetype chemistry font deposited at OSC, but is it "standard"? I ask because at the WWW conference at All ISO standards for fonts cover only letters and other glyphs used to write down ordinary words. No symbol font of any kind has ever been standardized. There are some quasi-standards like the PostScript symbol set, but they are probably not very useful for chemists. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) -------------------------------------------------------------------------------