From chemistry-request@server.ccl.net Mon Oct 9 05:44:47 2000 Received: from atom.cem.uct.ac.za (hydrogen.cem.uct.ac.za [137.158.164.149]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA13843 for ; Mon, 9 Oct 2000 05:44:35 -0400 Received: from sodium.cem.uct.ac.za (sodium.cem.uct.ac.za [10.10.10.11]) by atom.cem.uct.ac.za (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id LAA21400 for ; Mon, 9 Oct 2000 11:43:12 +0200 (SAST) Date: Mon, 9 Oct 2000 11:43:12 +0200 (SAST) From: Chas Simpson X-Sender: csimpson@sodium.cem.uct.ac.za To: chemistry@ccl.net Subject: chloroform solvent simulation difficulties Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All, I am trying to simulate (with MD) a chloroform solution using periodic boundary conditions in an NVE ensemble. The simulation of chloroform is well documented in literature but I am still unable to get it to stablise correctly. I heat the system up to 288K from 200K and equilibrate in an NVT ensemlbe at 288K with no problems. When I try and equilibrate in an NVE ensemble, the temperature jumps to about 350K no matter what I try. (I am running these simulations using CHARMM and using SHAKE to constrain the motion of the hydrogen atoms). My first question is how can I reduce the temperature in an NVE simulation, ie not just transfer the kinetic energy to potential energy but to actually reduce the kinetic energy term..... if that's possible/legal(!!)? Or alternatively is there something obvious that I am doing wrong? My second question is I am using particle mesh Ewald summations to treat the long-range nonbonded interactions. Charmm complains and says that I must specify the frequency for stopping the translation and rotation of the molecules during the simulation. Why is this necessary and what frequency should be used? And finally charmm automatically stops the translation and rotation of the molecules during heating. Why is this necessary? Thanking you in advance for any help (which will be GREATLY appreciated!!). Kind regards Chas simpson@psipsy.uct.ac.za From chemistry-request@server.ccl.net Mon Oct 9 07:15:25 2000 Received: from mail-a.bcc.ac.uk (mail-a.bcc.ac.uk [144.82.100.21]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA15088 for ; Mon, 9 Oct 2000 07:15:24 -0400 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-a.bcc.ac.uk with SMTP (Mailer) with ESMTP; Mon, 9 Oct 2000 12:15:03 +0100 Sender: mb@ucl.ac.uk Message-ID: <39E1B5EF.42C2256B@ucl.ac.uk> Date: Mon, 09 Oct 2000 13:11:27 +0100 From: Michael Brunsteiner Organization: University College London X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Chas Simpson CC: chemistry@ccl.net Subject: Re: CCL:chloroform solvent simulation difficulties References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Chas Simpson wrote: > > Hi All, > > I am trying to simulate (with MD) a chloroform solution using periodic > boundary conditions in an NVE ensemble. The simulation of chloroform is > well documented in literature but I am still unable to get it to stablise > correctly. I heat the system up to 288K from 200K and equilibrate in an > NVT ensemlbe at 288K with no problems. When I try and equilibrate in an > NVE ensemble, the temperature jumps to about 350K no matter what I try. > (I am running these simulations using CHARMM and using SHAKE to constrain the > motion of the hydrogen atoms). > My first question is how can I reduce the temperature in an NVE > simulation, in an NVE simluation the temperature should depend (in the long run) on the density only (and on the interaction potential parameters of course, but i assume you use the standard non-bonded parameters provided by charmm anyway ...) > ie not just transfer the kinetic energy to potential energy > but to actually reduce the kinetic energy term..... if that's > possible/legal(!!)? you are not supposed to/cannot do that ... the ratio between kinetic and potential energy is a constant for a given system in equilibrium (get yourself a textbook on statistical thermodynamics (MacQuarrie is good) and look for equipartition, energy ...) > Or alternatively is there something obvious that I am > doing wrong? no ... send me you input script ... > My second question is I am using particle mesh Ewald summations to treat > the long-range nonbonded interactions. Charmm complains and says that I > must specify the frequency for stopping the translation and rotation of > the molecules during the simulation. Why is this necessary and what > frequency should be used? And finally charmm automatically stops the > translation and rotation of the molecules during heating. Why is this > necessary? it is ALWAYS good to do this in the beginning of a simulation ... otherwise your thermostat may end up measuring the wrong temperature (apart from other more sublime problems) ... imagine your system uniformly translating through (periodic) space at a constant velocity in addition to the thermal motions .... your calculated kinetic energy would be rubbish ... (maybe thats also the reason for the temperature problem you describe above ...) concerning the frequency ... usually it should do to do it only once (i.e. in the beginning) ... so for a simulation with 100000 timesteps the frquency would be 1/100000 ... but in any case you should check whether charmm really does it ... it should say so in the output ... mic ============================================================== Man invented language to satisfy his deep need to complain. -- Lily Tomlin -------------------------------------------------------------- Michael Brunsteiner, Centre for Theoretical and Computational Chemistry, University College London mailto:m.brunsteiner@ucl.ac.uk, http://www.ucl.ac.uk/~uccambr/ -------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Oct 9 05:25:33 2000 Received: from c012.sfo.cp.net (c012-h001.c012.sfo.cp.net [209.228.13.92]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA13784 for ; Mon, 9 Oct 2000 05:25:28 -0400 Received: (cpmta 15200 invoked from network); 9 Oct 2000 02:23:18 -0700 Date: 9 Oct 2000 02:23:18 -0700 Message-ID: <20001009092318.15199.cpmta@c012.sfo.cp.net> X-Sent: 9 Oct 2000 09:23:18 GMT Received: from [194.249.5.10] by mail.altavista.com with HTTP; 09 Oct 2000 02:23:18 PDT Content-Type: text/plain Content-Disposition: inline Mime-Version: 1.0 To: chemistry@ccl.net From: Marina Ros X-Mailer: Web Mail 3.8.0.10 Subject: Mg2+ Dear CCLers, I'm a beginner in Molecular Modeling and I would gratly appreciate if someone could help me solving the following problems: a) The enzymatic system I'm dealing with contains several Mg2+ ions and I don't know how to evaluate them since the FF I'm been using is not parametrized for Mg2+ b) Should I add counterions or not? Why would be adding of counterions beneficial? Thanks. _______________________________________________________________________ Free Unlimited Internet Access! Try it now! http://www.zdnet.com/downloads/altavista/index.html _______________________________________________________________________ From chemistry-request@server.ccl.net Mon Oct 9 09:12:55 2000 Received: from hscmg02.hou.ucarb.com (hscmg02.hou.ucarb.com [144.68.4.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA15707 for ; Mon, 9 Oct 2000 09:12:54 -0400 Received: by hscmg02.hou.ucarb.com with Internet Mail Service (5.5.2650.10) id ; Mon, 9 Oct 2000 08:11:59 -0500 Message-ID: <4ADF6858B3A5D311AE2800805F5768AB52DD24@sctms03.sct.ucarb.com> From: "Smith JA (Jack)" To: chemistry@ccl.net, "'SA KUEHL'" Subject: RE: overlap integrals Date: Mon, 9 Oct 2000 08:11:55 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.10) Content-Type: text/plain > I am looking forroutines which calculate overlap integrals and other > one and two electron properties between different atoms in a Slater > basis set as a function of interatomic distance. Programs like this > were available through the QCPE but are now listed as unavailable. > Rather than to use overlap tables, I would rather have a program at > my disposal. Does any one have a working version of working > copies of QCPE 117, 118, 119, 202, 153. > Scott: I don't have the QCPE routines, but I do have my own routines for all the 1-center 1- and 2-electron STO integrals and most of the 2-center 1-electron integrals for arbitrary orientations (i.e., not just diatomics). They were written during the mid-70's in Fortran. The routines are based on extensive notes prepared by Frank Harris (I don't know if these notes were ever formally published). Most of the algorithms are based on recursion formulae, so there is no upper limit on the n,l,m quantum numbers. They are part of a larger program called PHATPSY which implements a "projected atoms approach to large and extended systems". I can send you the source if you're interested. - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jack A. Smith || Union Carbide || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-4672 P.O. Box 8361 || S. Charleston, WV 25303 || smithja@ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Mon Oct 9 04:05:55 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA13527 for ; Mon, 9 Oct 2000 04:05:52 -0400 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Mon, 9 Oct 2000 10:05:19 +0200 Message-ID: <008701c031c7$f3a67800$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: "Massimo Ottonelli" CC: References: <39D4E43A.167E@feynman.chem.rochester.edu> Subject: Re: CCL:charge visualization Date: Mon, 9 Oct 2000 10:07:21 +0200 > Dear CCLers, > > I am interested to plot the charge (for example as a sphere centred on > the nuclear position) of a molecular structure. > At yours knowledge there is any free program (available from the net) > for do that? > > > Thanks, in advance > Massimo >From: Massimo Ottonelli Not the usual solution (when the charge is plotted in a surface) what Mol2mol can do in conjunction with POV-Ray: a vector model can be colored by the charges (or any other atom properties), see the [begin jkl@ccl.net Moderator intervention: moved image from e-mail to web side] http://www.ccl.net/images/gpen4_na.jpg for the image of penicillin. [end jkl@ccl.net Moderator intervention: moved image from e-mail to web side] However, Mol2Mol is not a free program, look at http://www.compuchem.com/mol2mol.htm Sincerely T.E. Gunda -------------- Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm From chemistry-request@server.ccl.net Mon Oct 9 09:29:35 2000 Received: from mserv3.dl.ac.uk (root@mserv3.dl.ac.uk [148.79.80.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA15925 for ; Mon, 9 Oct 2000 09:29:34 -0400 Received: from dl.ac.uk (tca8.dl.ac.uk [193.62.112.106]) by mserv3.dl.ac.uk (8.9.3/8.9.3/[ref postmaster@dl.ac.uk]) with ESMTP id OAA01295 for ; Mon, 9 Oct 2000 14:29:21 +0100 Sender: H.J.J.VanDam@dl.ac.uk Message-ID: <39E1C787.E8EA2551@dl.ac.uk> Date: Mon, 09 Oct 2000 14:26:31 +0100 From: Huub van Dam Organization: CCLRC Daresbury Laboratory X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V5.0 alpha) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:MAX PLANCK, QUANTUM THEORY References: <39D917D7.177F6EDB@trentu.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit elewars wrote: > (2) Have there been any announcements of the big celebrations that must > surely be planned for the work that marked the transition from classical > to modern physics, revolutionized much of science, and laid the > foundations of new industries? Not as far as I know. I haven't even heard of anything to commemorate the 75th anniversary of the Schroedinger equation next year... Huub -- ======================================================================== Huub van Dam E-mail: h.j.j.vandam@dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD ======================================================================== From chemistry-request@server.ccl.net Mon Oct 9 11:52:36 2000 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA16697 for ; Mon, 9 Oct 2000 11:52:35 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA24805; Mon, 9 Oct 2000 11:56:09 -0400 (EDT) Date: Mon, 9 Oct 2000 11:56:08 -0400 From: Rick Venable To: Chas Simpson cc: chemistry@ccl.net Subject: Re: CCL:chloroform solvent simulation difficulties In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 9 Oct 2000, Chas Simpson wrote: > I am trying to simulate (with MD) a chloroform solution using periodic > boundary conditions in an NVE ensemble. The simulation of chloroform is > well documented in literature but I am still unable to get it to stablise > correctly. I heat the system up to 288K from 200K and equilibrate in an > NVT ensemlbe at 288K with no problems. When I try and equilibrate in an > NVE ensemble, the temperature jumps to about 350K no matter what I try. (I > am running these simulations using CHARMM and using SHAKE to constrain the > motion of the hydrogen atoms). > > My first question is how can I reduce the temperature in an NVE > simulation, ie not just transfer the kinetic energy to potential energy > but to actually reduce the kinetic energy term..... if that's > possible/legal(!!)? Or alternatively is there something obvious that I am > doing wrong? I recommend running some NPT simulations first, to ensure that your chosen density is consistent with the molecular potential. Also, be careful about system size; a rule of thumb is that you need 500 particles or more to get good stability. Your unit cell edge should probably be on the order of 40 A as opposed to 20 A, for instance. You should extract and analyze and/or plot the system Hamiltonian for both your NVT and NVE simulations; for NVE this is ETOT (KE+PE) which MUST be constant (flat) for a valid NVE simulation. The Hamiltonian for NVT depends on the method chosen; it's the term labeled XTLT for NVT done with the extended system (CPT LEAPFROG), and the Total Energy term printed in the optional data file (IUNO) for the NOSE method. Again, it should be flat, i.e. no apparent upward or downward drift; if not, it indicates a problem with energy conservation. As noted, there are a couple different ways of doing NVT simulations in CHARMM, and they are not particularly straightforward. An alternative is to use the more classic equilibration within CHARMM (non-zero IEQFRQ), using Gaussian assignment of velocities. I typically use something like ieqfrq 500 iasors 1 ichecw 1 twindh 5.0 twindl -5.0 This would assign velocities every 500 steps if T is more than 5 deg away from the target (FINALT), while the other 499 steps are propagated using standard NVE Verlet. This won't help if your volume (i.e. density) is not correct, however. > My second question is I am using particle mesh Ewald summations to treat > the long-range nonbonded interactions. Charmm complains and says that I > must specify the frequency for stopping the translation and rotation of > the molecules during the simulation. Why is this necessary and what > frequency should be used? And finally charmm automatically stops the > translation and rotation of the molecules during heating. Why is this > necessary? The net translation and rotation of the entire system are removed, and not that of individual molecules; the contributions from these 6 global degrees of freedom are redistributed over the remaining degrees of freedom within the system. Because of consistent errors probably related to shifting charges to a uniform grid for the mesh, it is necessary to do this regularly when using PM Ewald within CHARMM. Otherwise, a published phenomenon termed "the flying ice cube" can occur, where the entire system is being translated through space. This is done automatically when velocities are assigned every IHTFRQ (or IEQFRQ) steps, but NTRFRQ must be set explicitly for use with PM Ewald. As noted in the .doc file, the step frequency should be less than IPRFRQ to avoid an error exit. I've used ntrfrq 2500 iprfrq 5000 for simulations using PM Ewald electrosatics. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov )