-------- Original Message -------- Subject: Gromacs Date: Wed, 12 Jul 2006 20:14:52 +0800 From: PAUL NEWMAN <[EMAIL PROTECTED]> To: [EMAIL PROTECTED]
Dear David van der Spoel: I have a question about your web site (http://www.csc.fi/chem/courses/gmx2004/exercises/index.html). You give files to make a simulation of LJ-system in reduced units (Argon). I modified them in orde to reproduce the values of Mol. Phys. 78, 591-618 (reduced temperature= 5, reduced density = 0.4, it's in the attached file page 595). I simulated the system and I got the value close to the right pression, but the answer was wrong for the LJ potential (I got almost the potential but times 1000). I tried various other values and I got the same thing. I don't know where the error is?. I send you my grompp.mdp, conf.gro and topo1.top (Please see attached file). What i did is: * grompp.mdp.- I set up reduced temperature= 5, rcut-off =4 (rvdw), and Temperature coupling = Berendsen. * conf.gro.- I generated the initial positions as SC also in reduce units (simple cubic). reduced density = 0.4 (864 atoms and box size 12.92660x12.92660x12.92660) . * topo1.top.- I set up epsilon=1, sigma=1 and mass=1, it 's almost the same file in your web site. I just changed the number of particles (864 atoms) But I can't figure out what is wrong. Could you help me? Have you done any simulation in reduce units and checked them out?,if so, If it isn't too much to ask, could you send them to me . I'm sorry for bothering you about things, you might think, they are trivial questions. Thanks in advance. P.S.: gromacs gives the pression in bar ===> presion [in reduced units ] = 16.6054*pression (in md.log file). Is it right? I calculated the pression in this way. And i send you my md.log file. -- Cheers, Paul C.L. [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> / [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> National Tsing Hua University (清�A大�W) <http://www.nthu.edu.tw/> �x�x你的�兔� I appreciate your help. Thanks! Os agradezco la ayuda. Gracias! -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
