[gmx-users] Trjconv error
shima_arasteh2001 at yahoo.com
Tue Jun 19 10:41:46 CEST 2012
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.
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?
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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