On 19/06/2012 5:49 PM, Shima Arasteh wrote:
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?
We don't know what you've done. Try it and see... the whole purpose is
whether you like the form of what you see, right?
Mark
Thanks for your help.
Sincerely,
Shima
------------------------------------------------------------------------
*From:* Mark Abraham <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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.
Mark
How may I solve it? Anybody may suggest me any solution please?
I would be so thankful for your suggestions.
Sincerely,
Shima
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