Another way to check your density is to load your prmtop and rst7 in ParmEd, and run the “summary” command. Also, cpptraj can print the density too.
Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
Department of Chemistry
Stanford University
Twitter: .vwcruzeiro
On Jul 18, 2023, at 8:41 AM, David A Case via AMBER <amber.ambermd.org> wrote:
On Mon, Jul 17, 2023, Yang, Li-Yen via AMBER wrote:
Do you by any chance know how to make a NVT ensemble simulation run to
output the density value in the output file?
It seems like simulations with NPT ensemble will include density in the
output file, but not the ones with NVT ensemble.
You can generally "trick" Amber into reporting the pressure/density in NVT:
set ntb=2, ntp=1, barostat=1, taup=9999999. The large value of taup will
prevent any volume changes, but still print the info you want.
This may not work with constant pH, if it checks for NTP in a simple fasion.
You might need to modify the code to skip the error check.
....dac
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Received on Wed Jul 19 2023 - 08:30:02 PDT
