From justin@ukans.edu Wed Jun 9 22:53:36 1999 From: justin@ukans.edu (Justin Bradford) Date: Wed, 9 Jun 1999 16:53:36 -0500 (CDT) Subject: [dnd] MD aspect of DND Message-ID: I had seen references to DND before, and I had thought it was just a model rendering program, but I just noticed the MD simulation parts of it today. (Note: I have not run the program. I was just browsing the documentation.) Well, I'm very interested in working on the simulation code. I haven't had a chance to really look at what's there, but if the current programmer(s) could outline the current implementation, future plans, etc, I would appreciate it. Justin Bradford justin@ukans.edu From yoo@theoalpha.korea.ac.kr Wed Jun 9 01:30:23 1999 From: yoo@theoalpha.korea.ac.kr (SooHaeng Yoo) Date: Wed, 9 Jun 1999 09:30:23 +0900 (KST) Subject: [dnd] MD aspect of DND In-Reply-To: Message-ID: Hi ^^ Justin Bradford I'm a main developer of DND program. Call me "SooHaeng". On Wed, 9 Jun 1999, Justin Bradford wrote: > Well, I'm very interested in working on the simulation code. I haven't had > a chance to really look at what's there, but if the current programmer(s) > could outline the current implementation, future plans, etc, I would > appreciate it. Currently, if you want to take a part in the development of DND program, you need CVS login id. Therefore, if you want CVS login id, please contact with Jeff (bizzaro@bc.edu). I will make snapshots for someone who doesn't have CVS login id. If you hesitate to register DND program developer list and mailing list, you can use snapshots firstly. I have two developers. One is Kenneth Geisshirt and the other is Nikolaos Margaritis . The dnd version 0.5.1 ,which is in CVS, has a bug of the calculation of potential energy. But I use water box in which there are 125 tip3 molecules to test the molecular dynamics simulation in DND. The future plan is that DND includes the MD, energy minimization, building Molecules by mouse-picking and drug design module anything else. I hope that you are a family of DND project. I expect that you advise me about DND project to get more good results. Have a good day! From SooHaeng Yoo. From bizzaro@bc.edu Thu Jun 10 11:26:06 1999 From: bizzaro@bc.edu (J.W. Bizzaro) Date: Thu, 10 Jun 1999 10:26:06 +0000 Subject: [dnd] MD aspect of DND References: Message-ID: <375F92BE.45129EC6@bc.edu> SooHaeng Yoo wrote: > > Currently, if you want to take a part in the development of DND program, > you need CVS login id. Therefore, if you want CVS login id, please contact > with Jeff (bizzaro@bc.edu). I will make snapshots for someone who doesn't > have CVS login id. If you hesitate to register DND program developer list > and mailing list, you can use snapshots firstly. As Justin would have told you, if I did not, he is a Loci developer and has an account on TOL. So, he's okey dokey :-) > The dnd version 0.5.1 ,which is in CVS, has a bug of the calculation of > potential energy. But I use water box in which there are 125 tip3 > molecules to test the molecular dynamics simulation in DND. > I'm curious about the algorithm and force field being used for DND. I'm familiar with CHARMm and AMBER, which are both commercial. Many of the most common MD programs in fact have a common "ancestry". Where does DND fit in? Are there any journal references to check out? :-) Jeff -- J.W. Bizzaro mailto:bizzaro@bc.edu Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ -- From justin@ukans.edu Thu Jun 10 18:07:25 1999 From: justin@ukans.edu (Justin Bradford) Date: Thu, 10 Jun 1999 12:07:25 -0500 (CDT) Subject: [dnd] MD aspect of DND In-Reply-To: <375F92BE.45129EC6@bc.edu> Message-ID: > > The dnd version 0.5.1 ,which is in CVS, has a bug of the calculation of > > potential energy. But I use water box in which there are 125 tip3 > > molecules to test the molecular dynamics simulation in DND. > > > > I'm curious about the algorithm and force field being used for DND. I'm > familiar with CHARMm and AMBER, which are both commercial. Many of the most > common MD programs in fact have a common "ancestry". Where does DND fit in? > Are there any journal references to check out? I haven't had the chance to dig through the code for DND yet, but I was wondering the same thing. Do you use a fast multipole algorithm or something related? They are nearly O(N) for the number of molecules in the simulation. Furthermore, a group at Duke has done a lot of research on the topic and come up with a distributable parallel version. Both SIgMA and NAMD use their library. I'll check the license on it, but regardless, the algorithm is well documented and it would be possible to reimplement. This is the homepage for the Duke library. http://www.ee.duke.edu/Research/SciComp/Docs/Dpmta/ Justin From yoo@theoalpha.korea.ac.kr Wed Jun 9 22:35:16 1999 From: yoo@theoalpha.korea.ac.kr (SooHaeng Yoo) Date: Thu, 10 Jun 1999 06:35:16 +0900 (KST) Subject: [dnd] About Parameter and Topology. In-Reply-To: <375F92BE.45129EC6@bc.edu> Message-ID: Hi ^^ On Thu, 10 Jun 1999, J.W. Bizzaro wrote: > I'm curious about the algorithm and force field being used for DND. I'm > familiar with CHARMm and AMBER, which are both commercial. Many of the most > common MD programs in fact have a common "ancestry". Where does DND fit in? > Are there any journal references to check out? I referred the 3 books to develop MD for DND. 1) Understanding Molecular Simulation by Daan Frenkel & Berend Smit. 2) Computer Simulation of Liquids by M.P. Allen and D. J. Tildesley 3) The art of Molecular Dynamics Simulation by D. C. Rapaport I used the CHARMm force field. I don't know whether the parameter file and the topology file are used for DND. Do you think that I should make a parameter file (or format) and topology file (or format) for DND ? Currently I will use the simple algorithm to simulate of Molecules and then I will include better algorithms. From SooHaeng Yoo. From yoo@theoalpha.korea.ac.kr Wed Jun 9 22:45:57 1999 From: yoo@theoalpha.korea.ac.kr (SooHaeng Yoo) Date: Thu, 10 Jun 1999 06:45:57 +0900 (KST) Subject: [dnd] About fast multipole algorithm In-Reply-To: Message-ID: On Thu, 10 Jun 1999, Justin Bradford wrote: > Do you use a fast multipole algorithm or > something related? They are nearly O(N) for the number of molecules in the > simulation. Furthermore, a group at Duke has done a lot of research on > the topic and come up with a distributable parallel version. Both SIgMA > and NAMD use their library. I'll check the license on it, but regardless, > the algorithm is well documented and it would be possible to reimplement. > > This is the homepage for the Duke library. > http://www.ee.duke.edu/Research/SciComp/Docs/Dpmta/ I used the combination of verlet and cell lists (Ref: Understanding Molecular Simulation by Frenkel & Smit, Appendix C). The source file is cell.c at $(dnd top dir)/workspaces/md/src. Currently I didn't include the long-range interactions. If I have enough time, I will make the interface codes between DPMTA and DND. From SooHaeng Yoo From markoni@otenet.gr Tue Jun 15 03:53:05 1999 From: markoni@otenet.gr (Nikolaos Margaritis) Date: Mon, 14 Jun 1999 22:53:05 -0400 Subject: [dnd] install proplem References: Message-ID: <99061423185000.16348@aristotle.local> On Sat, 29 May 1999, you wrote: >Hi ^^ Niko. > > Did you succeed in compiling dnd program? > ^^ Actually, the dnd program compiles fine. Also it installs ok and it produces a quite neat rpm package. Unfortunately, It gives me a segmentation fault when I try to run it. Also, there seems to be a little problem with dnd-devel. This is what I get just after the install stage (i.e. the %post stage of the rpm spec file): Finding provides... Finding requires... ldd: warning: you do not have execution permission for `/var/tmp/dnd-0.5.1-root/usr/lib/libdndmd.so.0.0.0' ldd: warning: you do not have execution permission for `/var/tmp/dnd-0.5.1-root/usr/lib/libdndws.so.0.0.0' This happens because these lib files are installed with chmod 644 instead of 755. > >On Sun, 30 May 1999, Nikolaos Margaritis wrote: > >> there are meant to be some files installed in /usr/local/share/dnd but >> none was installed there. > >The files, that should be installed in /usr/local/share/dnd, are >dnd-file-loader.desktop and dnd-md.desktop from $(dnd-src >dir)/workspaces/md/gui and url-properties.desktop from $(dnd-src >dir)/workspaces/url-properties. Still, I cannot find those files. How are they meant to be installed? > >The files in $(dnd-src dir)/workspaces/url-properties are from >GNOME-control-center. Actually GNOME is not my GUI. KDE is mine, but I installed every GNOME bit I should have installed. Did I probably miss something? If yes, should that not be mentioned in the spec file (and probably add another Require entry in the spec?) Could you explain, please? > >I update the INSTALL file. Please remember that dnd.directory file is >important to run "dndcc". > To run dnd program, please type 'dndcc' which means 'dnd-control-center'. this is exactly what I do when I get the segfault... regards, Nikos PS. Should we use pgp signed mail? Or would that be unnecessary? What do you people think? -- Dr. Nikolaos A. Margaritis Agias Marinis 40, Larissa 41221, Hellas (Greece) Tel: +30(0)41 233568 URL: http://users.otenet.gr/~markoni From yoo@theoalpha.korea.ac.kr Mon Jun 14 08:28:51 1999 From: yoo@theoalpha.korea.ac.kr (SooHaeng Yoo) Date: Mon, 14 Jun 1999 16:28:51 +0900 (KST) Subject: [dnd] I will go to U.S. Message-ID: Hi ^^ I will go to the U.S. , so I see you again after 2 weeks. I need the time to prepare to go to the U.S. and should buy the computer and install Linux. ^^ Take care.