Gmx trjconv -fit

User discussions
1

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

Best Regards,
Lili

2

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

3

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

4

Mine is exactly like yours!

5

🤣same computer， you mean the same computer node?