Hi Thomas,
I get the point now. The input file was just an example. Yes, I have always
done 100 ns cycles, with each next cycle starting from the previous restart
file.
I should have changed it to ntf=2, but I didn't! Thanks for pointing it
out.
Best,
Mish
On Mon, May 15, 2023 at 10:44 AM Dickson, Callum via AMBER <
amber.ambermd.org> wrote:
> Hi Thomas,
>
> I wrote up my usual protocol for membrane protein MD here, in case parts
> of this are useful:
> https://github.com/callumjd/AMBER-Membrane_protein_tutorial
>
> I use semi-isotropic pressure scaling with surface tension term set to
> zero, this couples the X and Y allowing Z to vary (see 07_Prod.in file):
>
> ntp=3, csurften=3, gamma_ten=0.0, ninterface=2,
>
> To be conservative, the 100ns MD also uses skinnb=3.0 but provided the
> system is equilibrated, you can likely remove this since it slows down your
> simulation time.
>
> Regarding Monte Carlo barostat, this does result in a lower area per lipid
> than Berendsen, so the Berendsen barostat is preferred. However, I ran 300
> ns MDs for the Lipid21 paper and you can see the comparison between
> Berendsen and Monte Carlo barostats in the SI, in general the area per
> lipid drops by ~ 3 A^2, but does not result in a phase change of the
> membrane.
>
> Best,
> Callum
>
>
>
> -----Original Message-----
> From: Steinbrecher, Thomas via AMBER <amber.ambermd.org>
> Sent: Monday, May 15, 2023 10:15 AM
> To: David A Case <david.case.rutgers.edu>
> Cc: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] pmemd simulation exits abnormally
>
> This Message is from an External Sender. Do not click links or open
> attachments unless you trust the sender.
>
> 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
>
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!N3hqHg43uw!s1bb36bbBF43yti7SJYSyCaTukj-ygveCB7p5Me3pS94cpFvfI3vkikR1MaRZuUEgNtEMLCR16lw_AwFaxiM$
> _______________________________________________
> 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 - 10:00:02 PDT
