From: Maximilian Ebert (mebert_at_chemcomp.com)
Date: Fri Jul 24 2020 - 15:30:32 CDT
Hi there,
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:
1. minimize
2. Heating
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.
Any ideas?
Thanks,
Max
------
Maximilian Ebert
Application Scientist
Chemical Computing Group | www.chemcomp.com mebert_at_chemcomp.com | +1 (514) 393-1055 For support inquiries: support_at_chemcomp.com
------
Chemical Computing Group | www.chemcomp.com |
910-1010 Sherbrooke W., Montreal QC H3A 2R7, Canada | +1 514 393 1055
Manage Communications: www.chemcomp.com/Manage_Subscription.htm
-- Chemical Computing Group | www.chemcomp.com <http://www.chemcomp.com> | 910-1010 Sherbrooke W., Montreal QC H3A 2R7, Canada | +1 514 393 1055 Manage Communications: www.chemcomp.com/Manage_Subscription.htm <http://www.chemcomp.com/Manage_Subscription.htm>
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:13 CST