[gmx-users] Trjconv error

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Jun 19 09:49:56 CEST 2012

Thanks for your reply.

I entered the trjconv as the workflow of  http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

And I chose the 'system' as the chosen  group. Now, if I want to see the trajectory, am I supposed to load the mdfinal.xtc on the first frame ( 1stframe.pdb ), which I produced earlier? 

Thanks for your help.


 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, June 19, 2012 11:00 AM
Subject: Re: [gmx-users] Trjconv error

On 19/06/2012 4:13 PM, Shima Arasteh wrote:

Dear gmx users, I want to follow the workflow regarding to http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for the second step I enter the command as below:
trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb But I get the error:
 Index[232] 235 is larger than the number of atoms in the
trajectory file (234). There is a mismatch in the contents
of your -f, -s and/or -n files I don't have any index file, so what this error is talking about?
Then it must mean there's a mismatch in the contents of your -f and
    -s files... each must refer to the same system. Something about your
    past management of these two files makes your intended operation a
    nonsense, but we can't know what. If, for example, you chose
    xtcgroups in your .mdp file as something other than System, then
    they do not.


How may I solve it? Anybody may suggest me any solution please? 
> I would be so thankful for your suggestions.

gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120619/1f410629/attachment.html>

More information about the gromacs.org_gmx-users mailing list