Dear Amber Users,
I'm trying to calculate the self diffusion coefficient of a compound by simulating 500 molecules in a cubic box using NVE ensemble.
I first minimized, heated, cooled then equilibrated the box using NPT for 6 ns. Everything went fine. I then switched to NVE ensemble and this is where I have problems. When I visualized the simulation using VMD, the whole box drifted in one direction. This did not happen during NPT runs. The self diffusion coefficient is 50 time higher than expected (indicating the molecules are moving too fast?). I checked ETOT, TEMP, and VOL and everything seemed fine. ETOT is conserved during the NVE runs. Temperature was well equilibrated. I tried to restart the simulation with different NSCM flag but the same problem still occurred (I turned NSCM off (=0) during NPT equilibration and I used NTT=3 for temperature control).
I really appreciate any help I can get on this problem. I've been searching the forum archive but still haven't found a solution for it yet.
Thank you
Best regards,
Quynh Vo
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Received on Thu Jun 26 2014 - 16:00:02 PDT
