Thank you so much for your consideration. However, it still diverge even after correcting the number in 3rd column and using bond parameters. Also, using SHAKE is not helpful. I'm using single-precision GROMACS. Is it make this kind of problem? What else can I do try?
Thank you in advance for your kind instruction. Jae ---- Original message ---- >Date: Mon, 18 Sep 2006 11:13:03 -0400 >From: [EMAIL PROTECTED] >Subject: [gmx-users] re: n-hexadecane simulation >To: [email protected] > >You have #2 in the 3rd column which nmeans that you are not excluding >1-2, 1-3, or 1-4 Nonbonded interactions as you are intended to. Change >this value to a one instead of a two. That should fix your problem. >However, I would recommend that you set up the regular RB bonds like >this. That way you have the settings in case you want to stop >constraining bond lengths. > >Remove your [ constraints ] section and adding this: > >[ bonds ] > 1 2 1 0.15300E+00 0.33470E+06 > 2 3 1 0.15300E+00 0.33470E+06 > 3 4 1 0.15300E+00 0.33470E+06 > 4 5 1 0.15300E+00 0.33470E+06 > 5 6 1 0.15300E+00 0.33470E+06 > 6 7 1 0.15300E+00 0.33470E+06 > 7 8 1 0.15300E+00 0.33470E+06 > 8 9 1 0.15300E+00 0.33470E+06 > 9 10 1 0.15300E+00 0.33470E+06 > 10 11 1 0.15300E+00 0.33470E+06 > 11 12 1 0.15300E+00 0.33470E+06 > 12 13 1 0.15300E+00 0.33470E+06 > 13 14 1 0.15300E+00 0.33470E+06 > 14 15 1 0.15300E+00 0.33470E+06 > 15 16 1 0.15300E+00 0.33470E+06 > > >Chris. > >_______________________________________________ >gmx-users mailing list [email protected] >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 ======================================= Jae Hyun Park, Ph.D. Postdoctoral Associate 3221 Beckamn Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801 (Tel) 217-244-4353, (FAX) 217-244-4333 (E-mail) [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list [email protected] 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
