[gmx-users] Energy Conservation at the Beginning of a Production Run

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 28 21:10:09 CET 2019

Den 2019-03-28 kl. 20:53, skrev Kruse, Luke E.(MU-Student):
> Hello gromacs users,
> I am trying to simulate a peptide amphiphile with the CHARMM27 force field. To do this I have had to specify an additional bond type and bond, angle, dihedral, etc. parameters in the .itp files of the force field. Then, to check if I had done this correctly, I minimized the system, and ran a production run to generate an NVE ensemble, so that I could make sure the system was conserving energy appropriately. After looking at the energy vs time plot (produces with the gmx energy command), however, the system jumps from an initial energy, up ~20 kJ per mole and then conserves energy for the most part (slight drifting but seems tolerable relative to the initial discontinuity). Is this discontinuity a normal happenstance or a result of bad minimization?
Is that at step 0 in the simulation?

Please check options like
; Do not constrain the start configuration
continuation             = no

> Thank you!
> Luke

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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