Hi all,
There is one more thing that occured to me: My system has ntb = 2 set,
non-isotropic box scaling as recommended for membrane systems. Is it
possible that the system "drifts", since the membrane can freely change
shape in x-y direction as long as the total xy-area stays constant? This
wouldnt even be wrong physically, but I can imagine pmemd could have an
issue with that when splitting atoms into cells.
There is no semi-isotropic scaling in Amber that varies the z-box size
independent of the coupled x-y size, right?
>
> Just to check: how far into the simulation does this occur? Are you
> printing often enough to be sure that you are seeing all the volume
> changes that
> are taking place? (Especially if the error is early in the run.)
>
it happens more or less equally spaced during my 250ns production run, as
early as 30ns, or as late as 200ns into the run.
I'm certainly not printing often enough to see quick changes, if something
goes seriously wrong and destabilises the system in a few 1000s steps, I
would likely miss it (Im printing every 1 ns, which already creates huge
files).
>
> Note that vlimit is not checked on the GPU, but you can monitor the
> temperature via mdout. A couple things to try:
>
> 1. Have you done enough initial NVT eqilibration before switching to
> NPT?
> (I don't know what "enough" is here, but try 10 ns or so.)
>
the NVT equilibration is fairly short, but at the point here, we have done
20+ns of various restrained and unrestrained NPT equilibration, plus
typically more than 50ns of production runs. Density, Temperature and
Pressure all look fine the entire time, so it would be surprising (and very
worrying) if there could still be insufficient equilibration in the system
somehow...
> 2. Try NPT with the MC barostat to see if you get past this problem; you
> can switch to the Berendsen barostat later.
>
A past test had MC barostat and did not crash (N=1 observation), but I
thought that is not recommended for membrane simulations currently?
>
> Of course, it would be good if pmemd reported more details about what is
> going on -- at least exactly which dimension values were involved.
>
Yes, it would be helpful to know what pmemd expects here, or maybe to write
out the final coordinates when this condition occurs.
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Mon May 15 2023 - 07:00:03 PDT
