Dear all, Thank you so much for your suggestions. You don't know how much you guys are helpful.
First with Tsjerk's suggestion of using gmxdump, I got to know where the problem is. What I changed is ffgmx.atp and spc.itp. It is useful to pdb2gmx. But for grompp, it is not enough. I have to change the file of ffgmxnb.itp. For some reason, grompp reads this file and determin the mass of all atoms. So far, I got the mass of hydrogen changed to be 2 in the readable .tpr file. Of course, I could also see the mass showed correctly in the log file. Yes, Andres, I am very interested in the heavy water poteintial. Please email me the topology and modifed FF files. Thanks very much. David, What you thought is very resonable. That's why Andres said maybe I should consider more specific heavy water model. But at this moment, I am just trying to get some preliminary results. Thank you all, Joys ____________________________________________________________________________________ Don't get soaked. Take a quick peek at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
