# Gmx trjconv -fit

**URL:** <https://gromacs.bioexcel.eu/t/gmx-trjconv-fit/7657>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [November 16, 2023, 8:00pm UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-fit/7657 "2023-11-16T20:00:27Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Lili](https://avatars.discourse-cdn.com/v4/letter/l/b38774/32.png) [@Lili](https://gromacs.bioexcel.eu/u/Lili)\
**Post date:** [November 16, 2023, 8:00pm UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-fit/7657/1 "2023-11-16T20:00:27Z")

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Program: gmx trjconv, version 2021.3-MODIFIED  
Source file: src/gromacs/pbcutil/pbc.cpp (line 101)  
Function: numPbcDimensions(PbcType)::\<lambda()\>  
Hi,  
I am preparing gmx\_MMPBSA calculations after production mdrun,  
Bellow are my two commands. I first command survive but the second give errores as I pasted bellow.  
Command 1:  
gmx trjconv -s topol.tpr -f traj.xtc -o md\_noPBC\_center.xtc -pbc atom -center -n index.ndx  
Command 2:  
gmx trjconv -s topol.tpr -f md\_noPBC\_center.xtc -o traj\_fit\_centered.xtc -fit rot+trans -center -n index.ndx

I have tried both center and fit the Lig and Lig\_Protein. the second command always give errors.  
Anyone have the same issue with me and how to solve it?

Assertion failed:  
Condition: false  
Invalid pbcType in numPbcDimensions

For more information and tips for troubleshooting, please check the GROMACS  
website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)

Best Regards,  
Lili

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**Author:** ![shafa](https://avatars.discourse-cdn.com/v4/letter/s/cab0a1/32.png) [@shafa](https://gromacs.bioexcel.eu/u/shafa)\
**Post date:** [November 29, 2023, 10:14am UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-fit/7657/2 "2023-11-29T10:14:39Z")

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Hi Lili! I encountered this type of error yesterday. Turned out that the PBC identifier on my computer can’t read the trajectory correctly. Did you happen to do your mmpbsa calculation on a different computer rather than the one in which you did the production run? If so, try to do it on the same computer with the production run, that solved the problem for me.

Hope you find the solution soon!  
Best regards,  
Shafa

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<div class="post-metadata">

**Author:** ![Lili](https://avatars.discourse-cdn.com/v4/letter/l/b38774/32.png) [@Lili](https://gromacs.bioexcel.eu/u/Lili)\
**Post date:** [November 29, 2023, 10:27am UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-fit/7657/3 "2023-11-29T10:27:37Z")

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Hi Shafa,

Thanks for telling me :)  
I was using gromacs2023.1 for the production run and for gmx\_MMPBSA using one from 2021.

How about you?

Best regards  
Lili

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<div class="post-metadata">

**Author:** ![shafa](https://avatars.discourse-cdn.com/v4/letter/s/cab0a1/32.png) [@shafa](https://gromacs.bioexcel.eu/u/shafa)\
**Post date:** [November 29, 2023, 4:26pm UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-fit/7657/4 "2023-11-29T16:26:03Z")

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Mine is exactly like yours!

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<div class="post-metadata">

**Author:** ![Lili](https://avatars.discourse-cdn.com/v4/letter/l/b38774/32.png) [@Lili](https://gromacs.bioexcel.eu/u/Lili)\
**Post date:** [November 29, 2023, 5:18pm UTC](https://gromacs.bioexcel.eu/t/gmx-trjconv-fit/7657/5 "2023-11-29T17:18:16Z")

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🤣same computer， you mean the same computer node?