Hi Justin, Thank you for your reply. In fact , for this base pair of "Gb2 Cb2 1 0.000194e10 0.00217e4", whatever I do , the final result for this base pair is the same they will always separate from each other. Hence, I doubt whether this is because gromacs did not read my force field file at all.
I hope to get your further suggestions about that. Thank you . Yang ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Tuesday, November 25, 2008 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] course grain model for DNA He, Yang wrote: > Hi all users, > > when I am using the gromacs to simulate the course grain model for DNA, it > seems that the software doesn't recognize my force field file. I have > included all the bond and non-bond parameters in the bon.itp and nb.itp file. > > During my simulation , I found that the base pair for C-G which first are in > the balance distance always repel from each other so I try to increase the > value of epsilon to increase the dispersion between this pair but it still > did not work and the pair still repelled from each other after the > simulation . > > Then I tried like this " ; Gb2 Cb2 1 0.000194e10 0.00217e4 " > in my nb.itp file, I found that the simulation can still be carried on and > the simulation result is the same for this base pair. > Well, that line is commented out (;), so naturally it would have no effect. -Justin > So ,I got confused about this phenomenon . Can anyone of you give me some > suggestions? > > Thank you in advance. > > Yang > _______________________________________________ > 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 > -- ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ 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 _______________________________________________ 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
