Best idea is to ask the vmd people, they have their own emailing list.
Catch ya,
Dallas Warren
A polar bear is a Cartesian bear that has undergone a polar
transformation
On 28/04/2009, at 12:29 PM, "He, Yang" <[email protected]> wrote:
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
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_______________________________________________
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Please search the archive at http://www.gromacs.org/search before
posting!
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_______________________________________________
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