[gmx-users] input the .gro and .trr file to the VMD

[He, Yang]

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: 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.

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
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