On Tue, Jan 17, 2017, Chris Neale wrote:
>
> Sumary: Am I correct to presume that when running with pmemd the times
> listed by "TIME(PS)=" in the .out file match up with the frames listed in
> analyses output from cpptraj based on the .mdcrd trajectory file for
> irest=1 but that when irest=0 there is an additional value of "TIME(PS)="
> listed in the .out file for the very first frame that is not written out to
> the .mdcrd trajectory file?
No: in general, the energies printed in the mdout files are one time-step
off from those in the trajectory files. If you need to do an energy analysis
of snapshots, use the imin=5 option in sander, or energy analysis commands
in cpptraj or parmed.
....dac
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Received on Wed Jan 18 2017 - 13:00:03 PST
