I have done microsecond-long MD of several membrane simulations with ntb =
2 using both Amber 20 and 22 with no such issues, just in case it helps to
find the actual cause of this problem. I used these settings:
# prod.in
# prod at 300 K, constant pressure- 10ns
#
&cntrl
imin=0,
nstlim=5000000
dt=0.002,
irest=1,
ntx=5,
iwrap=0,
ntpr=50000,
ntwx=50000,
ntwr=50000,
ioutfm=1,
ntf=1,
ntb=2,
cut=10.0,
temp0=300.0,
ntt=3,
gamma_ln=2.0,
ntp=1,
pres0=1.0,
taup=1.2,
ntc=2,
&end
hope you are not trying to use TI functionally. I have been trying to
figure out this issue in a non-membrane protein-glycan system for GaMD
simulations. It looks like GaMD and TI code have something going on in my
system that abruptly changes potential energies to NAN or *** within just
10 steps, but randomly at some point during MD (earlier being within 50 ps
and longest being about 19 ns). CPU code, however, works fine.
Best,
Mish
On Mon, May 15, 2023 at 9:15 AM Steinbrecher, Thomas via AMBER <
amber.ambermd.org> wrote:
> in support of my last suggestion, I plotted the x and y box size and
> sqrt(x*y) for one of my simulations (one that completed, I should not have
> overwritten the halted ones...) and it certainly seems the later term is
> very constant while the x and y alone can vary more or less randomly by 10%
> or more.
>
> This would explain the seemingly random number of the crashes, as the box
> dimensions change almost in a random walk. This also would mean that every
> membrane simulation in pmemd.cuda should sooner or later crash with ntb=2
> since nothing stops the x and y dimensions from sooner or later changing
> too far.
>
> Maybe I'm on the wrong track here, but if the above is correct, should
> ntb=2 even be recommended for membrane simulations (which the manual does)?
> Sooner or later, the box will thin so much that one will see boundary
> artefacts.
>
> Would ntb=3 then be preferred? But that requires surface tension > 0 and
> lipid21 membranes should be run without surface tension afaik?
>
> Kind Regards,
>
> Thomas
>
>
> On Mon, May 15, 2023 at 3:50 PM Thomas Steinbrecher <
> thomas.steinbrecher.roche.com> wrote:
>
> > 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
> >
>
>
> --
> *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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 15 2023 - 08:00:02 PDT
