Dear David,
Thanks for your reply. I didn’t changed from NVT no NPT. I am performing a very slow heating of my system. This slow heating is causing vacuum bubbles on my water box. Is this related to Langevin thermostat or it will occur with any thermostat? Would you have any reference to recommend?
Thank in advance
Best Regards,
Hocine
Le 18 nov. 2022 à 17:12 +0100, David A Case <david.case.rutgers.edu>, a écrit :
On Thu, Nov 17, 2022, Hocine EL KHAOUDI ENYOURY via AMBER wrote:
Im performing an MD equilibration of a protein and I got the following
problem. I’m heating gradually my system (5K each 100000 steps) using a
Langevin thermostat, in the NVT ensemble. When I plot my data to check the
properties, I see that my potential energy and pressure don’t increase
linearly as other properties like kinetic energies. Is that normal? Would
you have any suggestion?
The resolution of your tiff file is really very poor, but it looks like
the pressure has a jump someplace in the middle, as though you changed from
NVT to NpT at that point. Is that possible? I don't see anything obviously
wrong with what you report, but this is exceptionally slow heating, compared
to usual protocols.
....good luck....dac
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Received on Mon Nov 21 2022 - 02:30:03 PST
