[gmx-users] Trjconv error

[Shima Arasteh]

Actually, I loaded the trajectory of md-run and saw the bonds stretching and behaves strangely . So, as Justin suggested, I decided to do as the work-flow of PBC. So I entered the commands as below:

 1.      First make your molecules whole if you want them whole

        trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc
 
2.      Cluster your molecules/particles if you want them clustered

3.      Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps.
    
    trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb

4.      Remove jumps if you want to have them removed using the first frame

        trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc

5.      Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step.

    trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc
 
6.      Put everything in some box.

        trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc

 7.      Fit if desired and don't use any PBC related option afterwards.

        trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc

Now I want to know if it is correct to load the final .xtc on the first frame to get a acceptable result? My main propose is to avoid the strange behavior of bonds. I'd like to know if I have done correctly?
However I need to say that I saw the final .xtc loaded on the first frame .pdb and got the normal movie.


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 12:38 PM
Subject: Re: [gmx-users] Trjconv error
 

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 <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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>


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