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

[Dallas B. Warren]

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" <yang.he at mavs.uta.edu> 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: 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
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> 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 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
> 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 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
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php