On 6/1/15 8:06 AM, soumadwip ghosh wrote:
Thanks Justin for your quick reply. What are the correct non-bonding settings for CHARMM to be used in the .mdp file?
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM I seem to have to post this information weekly...
Here is how the CNT molecule looks like prior to energy minimization. pre energy min CNT <https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing>
Yep, that's definitely wrong.
I am not continuing any of the equilibration steps anymore. As you can see the CNT structure is distorted badly. Please help me out. What settings do I need to change in order to avoid such distortion? Is there a possibility that the cnt topology was wrong to begin with?
The CNT topology is clearly wrong. It's probably missing some bonds or something. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
