From chemistry-request@ccl.net Sat Aug 9 11:09:04 2003 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h79F9298002923 for ; Sat, 9 Aug 2003 11:09:03 -0400 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 19lVLE-0001Ab-5d for chemistry|at|ccl.net; Sat, 09 Aug 2003 16:09:12 +0100 Received: from matpc18.mats.qmw.ac.uk ([138.37.43.64] helo=Ruzhen) by smtp.qmul.ac.uk with smtp (Exim 3.35 #5) id 19lVLD-00029e-00 for chemistry|at|ccl.net; Sat, 09 Aug 2003 16:09:11 +0100 Message-ID: <02d301c35e87$e3e11200$402b258a@Ruzhen> From: "Ru-Zhen Li" To: Subject: question about BABEL Date: Sat, 9 Aug 2003 16:07:03 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Sender-Host-Address: 138.37.43.64 X-QM-Scan-Accept: This message was accepted by ls_accept.so Dear all, Does anyone know how to use BABEL? I installed it on my computer(windows) and add the path to default path of window, and then I use babel -m to bring us the graphic interface, and I tried to convert .pdb to .che, but nothing happened, and no warning or error message either. can you please tell me why? Thank you in advance! best regards, ********************************************************************** Ms Ru-Zhen Li 0044-020-78826327 r.li|at|qmul.ac.uk Materials Department Queen Mary University of London E1 4NS From chemistry-request@ccl.net Fri Aug 8 14:58:27 2003 Received: from mx1.aist.go.jp (mx1.aist.go.jp [150.29.246.133]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h78IwQ98015170 for ; Fri, 8 Aug 2003 14:58:27 -0400 Received: from rpsmtp1.aist.go.jp by mx1.aist.go.jp with ESMTP id h78IwZK0027903; Sat, 9 Aug 2003 03:58:35 +0900 (JST) env-from (masakatsu-ito(at)aist.go.jp) Received: from smtp1.aist.go.jp by rpsmtp1.aist.go.jp with ESMTP id h78IwZ1H017894; Sat, 9 Aug 2003 03:58:35 +0900 (JST) env-from (masakatsu-ito(at)aist.go.jp) Received: from localhost by smtp1.aist.go.jp with ESMTP id h78IwYmO028086; Sat, 9 Aug 2003 03:58:34 +0900 (JST) env-from (masakatsu-ito(at)aist.go.jp) Date: Sat, 09 Aug 2003 03:58:08 +0900 (JST) Message-Id: <20030809.035808.229724605.Masakatsu Ito(at)aist.go.jp> To: chemistry(at)ccl.net Cc: markus(at)ks.uiuc.edu, masakatsu-ito(at)aist.go.jp Subject: Re: CCL:Reusing the NAMD code to build C++ simulation program From: masakatsu-ito(at)aist.go.jp In-Reply-To: References: <20030808.182940.115911130.Masakatsu Ito(at)aist.go.jp> X-Mailer: Mew version 2.3 on XEmacs 21.1.14 (Cuyahoga Valley) Mime-Version: 1.0 Content-Type: Text/Plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Markus, Thank you for your quick reply. As you wrote, Mindy, a sequential version of NAMD, helped me a lot. It was easy to reuse and modify its code. Actually we developed a C++ framework to generate variants of simulation programs and first examined its extensibility and validity by assembling the Mindy code and our code. The framework provides implementation of a replica-exchange method (which is also referred as parallel tempering), and one of its flexibility is the abstract class for a force field. Its subclass was derived to delegate the force field calculation to Mindy objects and to build an executable for replica-exchange method simulation. Now that we have measured the effectiveness of the simulation method with a small molecule, I like to challenge more larger molecules such as a protein-ligand complex. But force-field evaluation in such system has to be accelerated by an efficient algorithm like PME which is not implemented by Mindy. Thus I rephrase my question. Could somebody give me an explanation if it is possible to use the NAMD code instead of the Mindy one and how to incorporate its Charm++ code into a C++ framework. I would appreciate any suggestion or hints. Thanks in advance. Masakatsu Ito , Ph.D Grid Technology Research Center National Institute of Advanced Industrial Science and Technology Tsukuba Central 2, Tsukuba, Ibaraki 305-8568 Japan Phone : +81-29-861-5730 Fax : +81-29-861-5301 E-mail masakatsu-ito(at)aist.go.jp URL http://met.sourceforge.net/ From: Markus Dittrich Subject: Re: CCL:Reusing the NAMD code to build C++ simulation program > Dear Masakatsu, > > The TCBG group does offer an MD code called > MINDY which is derived form NAMD source code > written solely in C++. Maybe this will be of > help to you. > > http://www.ks.uiuc.edu/Development/MDTools/mindy/ > > > > cheers, > MARKUS > > On Fri, 8 Aug 2003 masakatsu-ito(at)aist.go.jp wrote: > > > Dear CCL'ers, > > > > I am wondering if it is easy to reuse the NAMD code to build C++ > > simulation program. My question might sound strange because NAMD is so > > famous for its high extensibility and object-oriented design with > > C++. But NAMD is actually coded in Charm++, an extended C++ for > > parallelization, so that the problem is that a programmer has to deal > > with Charm++ syntax in the NAMD code and its execution model for > > parallel computation. So, could somebody give me a brief explanation > > how the NAMD code can be incorporated into C++ framework, or if it is > > possible. > > > > I would appreciate any suggestion or references for a simulation > > program which is built by adding C++ code to the NAMD code. > > > > Thanks a lot in advance. From chemistry-request@ccl.net Fri Aug 8 14:55:42 2003 Received: from aquarius.ime.eb.br (aquarius.ime.eb.br [200.20.120.44]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h78Itg98015062 for ; Fri, 8 Aug 2003 14:55:42 -0400 Received: from epq.ime.eb.br (epq.ime.eb.br [200.20.120.217]) by aquarius.ime.eb.br (8.12.8/8.12.8) with ESMTP id h78ItlI5008113 for ; Fri, 8 Aug 2003 15:55:51 -0300 Received: from EPQ/SpoolDir by epq.ime.eb.br (Mercury 1.48); 8 Aug 03 16:01:13 -0300 Received: from SpoolDir by EPQ (Mercury 1.48); 8 Aug 03 16:00:44 -0300 Received: from epq.ime.eb.br (200.20.123.218) by epq.ime.eb.br (Mercury 1.48) with ESMTP; 8 Aug 03 16:00:42 -0300 Message-ID: <3F33F218.7040001(at)epq.ime.eb.br> Date: Fri, 08 Aug 2003 15:55:20 -0300 From: Teodorico Ramalho User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030313 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry(at)ccl.net Subject: B3LYP instead of HF ESP charges !!! Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCls Please, I would like to know if I can use B3LYP ESP charges from gas phase calculations to perform the free energy pertubation calculations. Because, these would be fixed charges. As comented in many force fields development papers, usually HF ESP charges are better than B3LYP values because the former compensate the lack of charge polarization in condensed phase simulations. Actually, I would like to justify the employ B3LYP ESP charges from gas phase calculations to perform free enrgy pertubation calculations. Could anyone give me any information or reference on the subject? Best wishes, Tedorico From chemistry-request@ccl.net Fri Aug 8 16:46:51 2003 Received: from mailrelay2.lanl.gov (mailrelay2.lanl.gov [128.165.4.103]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h78Kkp98017983 for ; Fri, 8 Aug 2003 16:46:51 -0400 Received: from norris-mail.lanl.gov (localhost.localdomain [127.0.0.1]) by mailrelay2.lanl.gov (8.12.9/8.12.9/(ccn-5)) with ESMTP id h78Kl0lP004603; Fri, 8 Aug 2003 14:47:00 -0600 Received: from lanl.gov (karlasgig.lanl.gov [128.165.72.19]) by norris-mail.lanl.gov (8.12.9/8.12.9/(ccn-5)) with ESMTP id h78Kl0Qg022973; Fri, 8 Aug 2003 14:47:00 -0600 Message-ID: <3F340BF0.3ADB5EC7*at*lanl.gov> Date: Fri, 08 Aug 2003 14:45:36 -0600 From: "Jason D. Gans" X-Mailer: Mozilla 4.76 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry*at*ccl.net CC: rlw28*at*cornell.edu Subject: Re: CCL:summary for program for superimposing (small) molecules ... References: <002a01c35d09$9d6a63f0$8400000a@laquicom02> <3F32AF2F.110FE643*at*cornell.edu> <3F32BBF3.1060002*at*chemi.muni.cz> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.35 The QMol RMSD differs from the Excel calculation because QMol sets the molecular center of mass to zero when you read in a structure. To read a structure verbatim, go to "Options | Read Coord options ..." on the menu bar and uncheck the "zero center of mass" option. Selecting the "Align B to A" button in the Alignment window will superimpose the two molecules with an optimal rigid body rotation and translation [see Acta Cryst. (1978). A34, 827-828 W.K. Kabsch for more information] that minimizes the (optionally) mass weighted RMSD. Regards, Jason B-Division Los Alamos National Lab > > I have a question as to how the program QMol calculates the RMSD of two > > structures. > > > > I used Excel to calculate the RMSD for two different conformations of > > the same molecule and compared the result that I get using QMol, and I > > get two different values, and I am wondering why that is. > > > > In Excel, I calculated the distances between the same two atoms in the > > two conformations, squared them, added them up, then divided by the > > number of atoms. > > After this, take the square root to get the RMSD. > > > > It looks to me like QMol does something different. > > isn't it possible that QMol produces for example mass-weighted RMS or > something similar? i can remember having similar problems (i.e. > different values of the RMSD on the same set of structures) with some > other programs (e.g. amber/ptraj, amber/carnal and vmd). maybe qmol > could be some kind of similar case... > From chemistry-request@ccl.net Fri Aug 8 19:17:43 2003 Received: from mxout2.cac.washington.edu (mxout2.cac.washington.edu [140.142.33.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h78NHg98021081 for ; Fri, 8 Aug 2003 19:17:43 -0400 Received: from hymn17.u.washington.edu (hymn17.u.washington.edu [140.142.15.131]) by mxout2.cac.washington.edu (8.12.9+UW03.06/8.12.9+UW03.06) with ESMTP id h78NHexu004339 for ; Fri, 8 Aug 2003 16:17:40 -0700 Received: from localhost (localhost [127.0.0.1]) by hymn17.u.washington.edu (8.12.9+UW03.06/8.12.9+UW03.06) with ESMTP id h78NHdGQ012385 for ; Fri, 8 Aug 2003 16:17:40 -0700 Date: Fri, 8 Aug 2003 16:17:39 -0700 (PDT) From: liaoyi[at]u.washington.edu To: chemistry[at]ccl.net Subject: need a practical computational book. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Hi, I can calculate those basic electronic properties such as energy, charge density, etc. with some softwares. I want to read a book that can tell me how to change these basic properties to some other specific properties such as hyperpolarizability. Can anybody recommend one? Also, does any software can give electron properties of a excited state? Thanks. From chemistry-request@ccl.net Sat Aug 9 18:36:33 2003 Received: from kafka.net.nih.gov (kafka.net.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h79MaX98009347 for ; Sat, 9 Aug 2003 18:36:33 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.9/8.12.9) with ESMTP id h79Majx9016394; Sat, 9 Aug 2003 18:36:45 -0400 (EDT) Date: Sat, 9 Aug 2003 17:57:30 -0400 From: Rick Venable To: Michael Crowley cc: Michael Chen , chemistry!at!ccl.net Subject: Re: CCL:EWALD PME problem In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable!at!nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 1 Aug 2003, Michael Crowley wrote: > I will check, but I am fairly sure that the > fft dims do not need to be a multiple of number of processors, > at least that was my intention. I got curious and ran some CHARMM tests (short MD) where I varied the number of processors and the integer grid size for the PM Ewald method (FFTX etc.) and noted that there doesn't seem to be a requirement for the grid sizes to be a multiple of the number of processors. I examined elapsed time and the average potential energy and fluctuations, and observed no problems when FFTX wasn't a multiple. I apologize if I misled anyone. However, there does seem to be a requirement to use 2**N processors only with PME, i.e. 2, 4, 8, 16, etc., at least with CHARMM; attempts to run with 6 processors gave the error message Process aborting... ***** LEVEL -5 WARNING FROM ***** ***** non 2**N PE count in transpose so I would have expected a similar message for an attempt to use e.g. 30 processors. As one might expect, my tests showed that the average potential energy varied slightly with the grid spacing. This suggests the grid size should probably be kept the same within a simulation project, in order to be using consistent force field parameters throughout. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable!at!nih.gov ALT email: rvenable!at!speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=