[gmx-users] Trjconv error

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 19 10:08:59 CEST 2012

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?


> Thanks for your help.
> Sincerely,
> Shima
> ------------------------------------------------------------------------
> *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.
> 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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