From nakiya@engin.umich.edu Wed Apr 15 15:38:36 1998 Received: from phoenix.engin.umich.edu for nakiya@engin.umich.edu by www.ccl.net (8.8.3/950822.1) id OAA02872; Wed, 15 Apr 1998 14:50:59 -0400 (EDT) Received: from localhost (nakiya@localhost [127.0.0.1]) by phoenix.engin.umich.edu (8.8.7/8.8.7) with SMTP id OAA17862 for ; Wed, 15 Apr 1998 14:50:57 -0400 (EDT) Date: Wed, 15 Apr 1998 14:50:56 -0400 (EDT) From: Naoko Akiya Reply-To: Naoko Akiya To: chemistry@www.ccl.net Subject: CCL: MD package - SUMMARY In-Reply-To: <199804131818.PAA04125@dfa.ifi.unicamp.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here is the question I posted a few days ago: > I am looking for an MD package that can do the following: > > - uses user-supplied potential models as well as built-in models > - does isothermal simulation with Nose-Hoover thermostat > - works on Unix, preferably HP > - calculates free energy > - lets the user follow the trajectory of a particular molecule from a > given initial condition > - can do multiple timestep integration > > If you have any suggestions for a particular MD package that does all > or some of the above, please let me know. FYI we are not looking into > polymers or macromolecules. I will summarize the responses if there is > any interest. Here are the replies: ----------------------------------------------------------------- From Dayong He Try to find the homepage of GROMACS, it is free for academic purpose, has many options: MD, NEMD, energy minimization, .... ----------------------------------------------------------------- From Simon Hogg You might want to look at TINKER http://dasher.wustl.edu I think it can do all those things, but I'm not a developer, so I'm not 100% sure. ----------------------------------------------------------------- From Jordi Villa Freixa A good package that allows easy implementation of user-supplied potential models is TINKER. You can found it in: http://dasher.wustl.edu/tinker/ ----------------------------------------------------------------- From Keith Refson The only program I can think of which will do this is DL_POLY. Info at http://www.dl.ac.uk/CCP/CCP5/dl_poly.html I believe it does nearly everything you want. The exception is to "calculate free energy" which is of course impossible in practice. You can calculate relative free energies of two systems in equilibrium using Gibbs ensemble or Grand Canonical monte Carlo or free energy along a constrained reaction co-ordinate using the potential of mean force method. I can't remember whether DL_POLY can do a PMF calculation or not, but I think it may. My own MD program, moldy does not have PMF, a multiple timestep, nor any "built in" models, but if you look at my web page I have links to other MD codes. http://www.earth.ox.ac.uk/~keith/moldy.html ----------------------------------------------------------------- From German Sastre Navarro I'm extremelly pleased with DL_POLY which I've been using for diffusion of hydrocarbons in microporous materials. It's a general MD code, extremelly flexible, and can run on a wide variety of machines, with one or many processors. If you're interested contact Dr. Will Smith at Daresbury Laboratory, U.K. : w.smith@dl.ac.uk ----------------------------------------------------------------- Thank you all for your response. After checking all the recommended programs (and others not listed above), however, I have come to a conclusion that none of them do everything I need. (Maybe I just need to collect more information about each program.) So if I do use them I will have to make substantial modifications/additions myself, in which case I may be better off just writing my own code... If anyone thinks otherwise, please let me know. Sincerely, Naoko =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (734) 764-7121 Ann Arbor, MI 48109-2136 fax (734) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=