Hi Mrinalini. Thank you for your suggestions. In my previous case, I never use the distance restraints . So I wonder whether you can provide me a sample for file of the disres.itp .In fact, I don't know much about this file' form and how to set values in the file.
Thank you. Yang ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mrinalini Puranik [EMAIL PROTECTED] Sent: Tuesday, November 25, 2008 3:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] course grain model for DNA If there is fraying at the edges only, you can impose distance restraints on some of the hydrogen bonds at the ends. You need to modify md.mdp to turn on distance restraints and have a new file called disres.itp that mentions the distances to be restrained. Hope this helps, Mrinalini On Wed, Nov 26, 2008 at 1:06 AM, He, Yang <[EMAIL PROTECTED]> 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. > > 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 > -- Mrinalini Puranik _______________________________________________ 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
