From: Maximilian Ebert (mebert_at_chemcomp.com)
Date: Fri Jul 24 2020 - 15:30:32 CDT
There seems to be an issue with step counting if the output frequency is set larger than the number of steps in a segment.
I ran a two step free md simulation of a fully solvated protein:
I did 500 steps of energy minimization and used a dcdfreq, xstfreq, outputMomenta, outputEnergies of 25000. This will not generate a dcd file for the minimization step. In the heating step I ran 100 ps which resulted in the expected two frames in the DCD. In total 50500 steps have passed at the end of the run. 500 minimization and 50000 heating.
I start the heating with the coordinates, velocities and extendedsystem of the minimization run. The stdout correctly says that firsttimestep is 500. I also use a callback function to output the energies in a cleaner output file. In this file I correctly see at the first write of the energies (after 25000 in the heating segment since outputEnergies is set to 25000) 25500 steps have been completed. However if I parse the header of the dcd the start value of the first frame is set to 25000 which omits the 500 steps of the energy minimization. I have never seen this when each step had at least one frame in a dcd.
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