if you did not do any NPT relaxation, then vacuum bubble are expected since
the initial model may not have been built with the exact correct density.
this is common when adding solvent around a solute. the bubble are not from
slow heating, but just indicate the need to equilibrate the box volume for
the system.
On Mon, Nov 21, 2022 at 5:17 AM Hocine EL KHAOUDI ENYOURY via AMBER <
amber.ambermd.org> wrote:
> 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 - 08:30:03 PST
