Hi, I just got this CG DNA model from a paper as well as the required parameters . What you think I should deal with the interactions about hydrogen bonding ? I have defined all the atoms' charge as 0 but still the repelling happened.
Yang ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, February 05, 2009 3:58 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] about the repelling of DNA base pair He, Yang wrote: > Hi all users, > > I am dealing with the CG DNA model and I just list the parameters for > non-bond potential blow: > > A T 1 0.0069 0.000004109 > > P P 1 0.000004352 4.352E-12 > > S S 1 0.000004352 4.352E-12 > > A A 1 0.000002177 1.0894852E-12 > > T T 1 0.000002177 1.0894852E-12 > C G 1 0.0097 0.000005422 > C C 1 0.000002177 1.0894852E-12 > G G 1 0.000002177 1.0894852E-12 > > A S 1 0.000004352 4.352E-12 > > A P 1 0.000004352 4.352E-12 > A C 1 0.000002177 1.0894852E-12 > A G 1 0.000002177 1.0894852E-12 > > T S 1 0.000004352 4.352E-12 > > T P 1 0.000004352 4.352E-12 > T C 1 0.000002177 1.0894852E-12 > T G 1 0.000002177 1.0894852E-12 > C S 1 0.000004352 4.352E-12 > C P 1 0.000004352 4.352E-12 > G S 1 0.000004352 4.352E-12 > G P 1 0.000004352 4.352E-12 > > S P 1 0.000004352 4.352E-12 > > You can see that the base pair potential is larger than the other pairs . But > I found when I run this case,using the command "ngmx", it always shows that > the matching base pair will repel from each other even I set the temperature > by 0K in the mdp.file . I have checked the base pairs' distance and > originally they are all in the equilibrium distance. > Then your model physics are unrealistic. Either the parameters are wrong, or your .mdp options are inappropriate. Do your nucleotides really just consist of three particles (base, sugar, and phosphate)? If so, you may be missing some of the subtleties of hydrogen bonding (which is an electrostatic interaction), and the geometry within the helix, and perhaps even causing excessive repulsion between the phosphate backbones. -Justin > Thank you for any suggestions 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 gmx-users-requ...@gromacs.org. > 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 gmx-users-requ...@gromacs.org. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
