you might want to read the tutorial on the Amber web page, it discusses
this exact issue (with pictures).
https://ambermd.org/tutorials/basic/tutorial13/index.php
On Wed, Nov 23, 2022 at 5:46 AM Hocine EL KHAOUDI ENYOURY <
hocine.el-khaoudi-enyoury.etu.u-paris.fr> wrote:
> Dear Pr. Simmerling,
>
> Thank you for your feedback. In fact, I see the vacuum bubbles. Would be
> appropriate to heat my system switching NVT and NPT? At he end, after the
> heating I will do a NPT equilibration to remove progressively the
> constraints
>
> Best Regards,
>
> Hocine
>
> Le 21 nov. 2022 à 17:14 +0100, Carlos Simmerling <
> carlos.simmerling.gmail.com>, a écrit :
>
> 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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>>
>
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Received on Wed Nov 23 2022 - 07:00:02 PST
