[gmx-users] input the .gro and .trr file to the VMD
yang.he at mavs.uta.edu
Tue Apr 28 04:26:27 CEST 2009
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.
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham [Mark.Abraham at anu.edu.au]
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.
> 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.
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
gmx-users mailing list gmx-users at gromacs.org
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-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users