What does gmx check tell you about the trajectory files that you are trying to analyze?

Hi Caroline Freitas . There are a number of factors that could have resulted in the type of error you got. Ensure the following. First, as Justin Lemkul l said, use gmx check to see if your trajectory is not corrupted (if you are new to GROMACS, have this command-line reference with you = manual.gromacs.org/documentation/2018/user-guide/cmdline.html#commands-by-name).

Next, if you see that your trajectory is not corrupted and GROMACS is indeed reading all the way to 100ns, see ensure that you actually selected your backbone in the RMSD. You might have selected some different parameters by accident. I checked your .xvg and I saw that you are not trying to center your protein (noPBC). This usually does not affect the RMSD at all, but might happen. It is hard for me to see this in the .xvg, but I think that you only have 10ns in there, not 100ns. Check your .xtc file, maybe a problem when you merged your .xtc (it appears that you performed the MD 10ns at a time). Otherwise, you might need to explain more about your inputs and steps for further help.

Can you show us the "gmx trjconv" flags/options you used to prepare your "md_noPBC.xtc" trajectory?

Let me know two things

1. Do you have several trajectory files? (Incase, if you have restarted the job or extend the run you might have several files. Check which file you taken for the analysis).

2. During RMSD analysis, how much time steps were shown in terminal to calculate the RMSD.

I hope you can rectify the error now.

Please try to covert your .xtc file to noPBC.xtc in case to correct the periodicity then use the converted one for analysis.

and ofcourse check it with gmx check.

thanks

Thank you all for help me. Bruno César Feltes I'll check .xtc file and try the gmx check too. In any case, I feedback you here.