GROMACS modification: Yes/No
I have completed the simulation of 200ns for my system and then check my .xtc file by
gmx check -f file.xtc then there is error in running gmx check
Magic Number Error in XTC file (read 1222875783, should be 1995)
My file.xtc has run upto 190ns without any error and for last 10 ns around 192ns it shows magic number error
Anybody can help me regarding this
What should I do ?
Is there a solution for this .xtc file
The header of each XTC frame contains this number to designate it as an XTC frame. For whatever reason, your file has completely different data there. If this happens half-way through the file, you can still rescue the earlier parts by reading and then writing to another file.
Unfortunately this means your file (i.e., disk storage) is corrupted in a major way. This can be due to a number of reasons, all of which are not part of GROMACS (Bad disk, bad controller, corrupted file system, multiple processes writing to the same file without proper locking, etc.)
If my file has corrupted, should I rerun the system for 200ns
Thank you for the suggestion
191ns trajectory out of 200ns is rescued but now don’t have .cpt file for completion of 200ns run.
suggest me how to write .cpt file upto 191ns
Unfortunately you can’t go back and recreate a checkpoint, since saving all checkpoints would be equivalent to storing full precision coordinates and velocities, which will take order-of-magnitude more space.
You CAN of course store full precision coordinates and velocities in a normal TRR trajectory if you want to, but that has to be decided before you start a simulation.
Although it’s not ideal, in particular for a large system it might not be the end of the world to continue a simulation by generating new velocities,