Hi Joys Yu, In addition to Tserks comments you might want to use a more specifically developed heavy water model. Here is a reference you may find usefull: An effective pair potential for heavy water - J. Raul Grigera The Journal of Chemical Physics -- May 8, 2001 -- Volume 114, Issue 18, pp. 8064-8067.
I have created a topology file based on these parameters for a cooperation I did some time back. If you are interested I can email the topology & modified FF fiels to you. Regards Andrés El Martes, 27 de Marzo de 2007 03:29, Joys Yu escribió: > Dear all, > > I would like to do simulation of bulk heavy water > (D2O). So first thing, I need to get the topology file > of D2O. In fact, I would like to use SPC H2O. I just > need to change the mass of H in H2O from 1.008 to > 2.016. > > I would like to use gromacs force field(#7). So I > revised ffgms.atp. I changed the mass of water > hydrogen from 1.008 to 2.016. > > When I use pdbtogmx to get the topology, it seems > fine. I have a bulk heavy water, which has 674 D2O. > Here is some of the running results from pdbtogmx: > > Now there are 674 residues with 2022 atoms > Making bonds... > Opening library file > /home/gromacs-d/share/top/aminoacids.dat > Number of bonds was 1348, now 1348 > Generating angles, dihedrals and pairs... > There are 0 dihedrals, 0 impropers, 674 angles > 0 pairs, 1348 bonds and 0 virtual > sites > Total mass 13501.164 a.m.u. > Total charge 0.000 e > > > The total mass for 674 D2O is correct: 674 * 20.03 = > 13501.164 > > Here is the topology file that I got for D2O: > > ; > ; File 'd2o.top' was generated > ; By user: Joys (1002) > ; On host: Boyang > ; At date: Mon Mar 26 20:15:57 2007 > ; > ; This is your topology file > ; Generated by genbox > ; > ; Include forcefield parameters > #include "ffgmx.itp" > > ; Include water topology > #include "spc.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include generic topology for ions > #include "ions.itp" > > [ system ] > ; Name > Generated by genbox > > [ molecules ] > ; Compound #mols > SOL 674 > > Everything seems fine here. Then I want to do a MD > simulation. I used grompp to get the .tpr. I could > also run it. But in the .log file, I found the mass of > the system is the mass of H2o ( about 12132) not > 13501.164. > > I got D2O topology from pdb2gmx correctly. But it > seems that grompp did not read in this topology. > > Can anybody kindly tell me where the problem is? What > should I do to get D2O topology? > > Many thanks, > Joys Yu > > > > > > > ___________________________________________________________________________ >_________ Looking for earth-friendly autos? > Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center. > http://autos.yahoo.com/green_center/ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 -- ---------------------------------------------------------------------- Dr. Andrés N. McCarthy Instituto de Física de Líquidos y Sistemas Biológicos (UNLP-CONICET-CIC) Depto. Cs. Biológicas - Fac. de Cs. Exactas - Univ. Nac. de La Plata 59-789, CP (1900) La Plata, Argentina Tel: +54-221-4254904 / +54-221-4233283 FAX: +54-221-4257317 e-mail: [EMAIL PROTECTED] web site: www.iflysib.unlp.edu.ar ---------------------------------------------------------------------- _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
