OK, I am going to try nscm=10 and see what happens. I see that nscm is 1000 by default. I'm using Amber 11.
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
________________________________________
From: Ismail, Mohd F. [farid.ou.edu]
Sent: Wednesday, November 14, 2012 2:38 PM
To: amber.ambermd.org
Subject: [AMBER] COM removed message and Energy Drift
I have a solvent box of 400 small organic molecules. I use GAFF for the parameters. The box is equilibrated with NPT until the density converged, and I got good density comparable to experimental value. I then use NVE simulation to get the diffusion.
I get the check COM velocity, temp: 0.000003 0.00(Removed) message all the time in the output file. But in this case, for the NVE run, the energy is drifting, i.e. it keeps increasing and doesn't seem like it is going to equilibrium. I tried doing NVT before going with NVE simulation, but after I returned to NVE the energy is still drifting.
Are these two (the COM removed message & energy drift) related?
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
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Received on Wed Nov 14 2012 - 13:00:03 PST
