[gmx-users] Trjconv error
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 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.
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