[gmx-users] editconf and genbox using method

[Marian Butu]

Thank you very much.
Trjconv works fine.

Marian

On Mon, Mar 9, 2009 at 1:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Mark Abraham wrote:
>
>> ----- Original Message -----
>> From: Nuno Azoia <nazoia at det.uminho.pt>
>> Date: Monday, March 9, 2009 21:52
>> Subject: Re: [gmx-users] editconf and genbox using method
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>
>> Hello!
>>>
>>> Your box isn't rectangular. Your problem is just VMD display the gro
>>> file with a rectangular shape. If you need to see your system properly
>>> try to transform your .gro file in a .pdb file first, using trjconv.
>>>
>>> Try trjconv -h to see the options
>>>
>>
>> I don't believe this is correct. That would be a bizarre thing for VMD to
>> do. Much more likely is that editconf actually selected a rectangular box,
>> genbox filled it, and VMD is displaying what's in the file.
>>
>>
> Actually, I've found trjconv to be necessary.  VMD indeed shows a
> rectangular box for my dodecahedral systems, if I have not used trjconv -pbc
> mol -ur compact.
>
> The transformation to .pdb, however, is unnecessary.  The .gro file can be
> processed in the same way.
>
> -Justin
>
> Mark
>> _______________________________________________
>> 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
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
> _______________________________________________
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090309/9b85a260/attachment.html>