GROMACS version:5.1.4
GROMACS modification: Yes/No
Dear all,
We have created replicas and want to combine the .gro files of these replicas to generate one .gro file. But when we use the command gmx trjcat for combining thsese .gro files, an error is occurred
Can not write a gro file without atom names For more information and tips for troubleshooting, please check the GROMACS website at Errors - Gromacs
Please suggest regarding this error and how to take average of .gro files of replicas to use one average file for further analysis.
If you are trying to create a multi-frame .gro file, just concatenate them with the Unix command cat. A .gro file is simply text.
If you want to generate a single frame from multiple coordinate files, again use cat but you will have to remove header and box vector lines in the middle of the file and update the number of atoms in the final .gro file on the second line.
Thank you for suggestion,
My aim is to generate one reference structure file for the flag -s from the replicas generated at different initial seed for velocities for the analysis because it seems complicated to do analysis for each replica and combine them for showing the average result of these replicas. can you also suggest me about the average of .xtc file from the replicas to generate one .xtc file?
Averaging trajectories doesn’t make any physical sense. If you want one reference for the calculations, use any of the .tpr files you already have. You can’t concatenate structures to make a single reference and averaging is unphysical.
Thank you for your suggestion