HI Mark, I am indeed using the coarse-graining atoms .What do you mean by " tell VMD to use suitable rules, or something similar." Do you have any fixed case about how to solve this problem in vmd?
Thank you very much. Yang ________________________________________ From: [email protected] [[email protected]] On Behalf Of Mark Abraham [[email protected]] Sent: Monday, April 27, 2009 7:00 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] input the .gro and .trr file to the VMD He, Yang wrote: > Hi all users, > > I want to get some snap shots from VMD through inputing my gro and trr file > to the VMD. But I always find that I can not get the bond connection among > the atoms and then, I try to use the dynamic bonds to solve this problem but > another problem is that when I define a value for the cutoff distance, the > bonds which don't exist among the atoms in the original shape will also come > up . VMD guess at bonds based on atom names and inter-atomic distances, so your .gro file isn't following the rules it expects. Either your structures are broken, or they're coarse-grained and you need to tell VMD to use suitable rules, or something similar. Mark > Except the dynamic method to figure out this problem, I wonder whether there > are other ways to fix this problem. > > Thank you for any suggestions. > > Yang > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected] 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 [email protected] 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
