Hi Ross:
There is also a very big GPU cluster at the center that would fit the sace.
However my grant is for a BluGeneQ (it was my choice because of PLUMED).
Had I known that before...
I need >200 replicas, if I want to continue with explicit water, so that my
own GPU machine is out of the game. However prof Simmerling made it clear
that now dwelling with implicit water for remd may just be the fruitless
way.
thanks
francesco
On Wed, Sep 11, 2013 at 3:42 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Francesco,
>
> For 'performance' you need at least 1 GPU per replica when running REMD on
> GPUs, it doesn't matter if these are in the same node, spread between
> nodes or a combination of the two providing your mpirun is setup to
> distribute threads correctly to different nodes. However, if you just want
> to test / debug REMD on GPUs you can overload a GPU, performance will suck
> but it will work. Just make sure the GPUs are NOT in compute exclusive
> mode.
>
> nvidia-smi -c 0
>
> Then just run the number of MPI threads to match the number of groups you
> have and they will get handed out in a round robbin fashion to the number
> of GPUs that are visible to those MPI threads, overloading as need be.
>
> All the best
> Ross
>
>
>
> On 9/10/13 11:03 PM, "Francesco Pietra" <chiendarret.gmail.com> wrote:
>
> >Hello Hai:
> >Can a debug trial be carried out on a shared memory GPU machine (the one I
> >use currently) or are multiple physical nodes required? With NAMD,
> >physical
> >nodes are needed.
> >
> >At any event, what you suggest is MD, i.e., at a single temperature. So
> >that the milliseconds are needed to hope to overcome the energy barriers.
> >
> >Thanks
> >francesco
> >
> >
> >On Tue, Sep 10, 2013 at 11:59 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> >> hi Francesco,
> >>
> >> If you can access to GPU cluster, you might want to try implicit
> >> solvent simulation (like igb=8) first. Instead of running expensive
> >> REMD, you can run multiple MD simulations (with different ig number or
> >> different starting structures). With GPU cluster and igb8, you might
> >> get about 500 ns/day.
> >>
> >> Hai
> >>
> >>
> >> On Tue, Sep 10, 2013 at 11:22 AM, Francesco Pietra
> >> <chiendarret.gmail.com> wrote:
> >> >
> >> > I was at your earlier papers. May I ask for a pdf of the 2013 cited
> >> > article? At our poor academy we do not subscribe that journal <
> >> > francesco.pietra.accademialucchese.it>.
> >> >
> >> > My aim was to hopefully arrive at a major cluster of conformations,
> >>if
> >> > any. It would be an improvement anyway on lack of useful diffraction
> >>by
> >> > this part of the protein (Following Modeller integration of lacking
> >> > portions, I have detached a portion of the six X-ray diffr
> >>indescribable
> >> > portions, planning to superimpose the T-remd-resulting cluster through
> >> the
> >> > few well described helical turns and delete the original). NMR - in my
> >> > hands - proved unable to treat the case. So, theory was left.
> >> >
> >> > It deals of a transmembrane protein, with the portions to model just
> >> > emerging from the bilayer. Nonetheless, I could also try implicit.
> >> >
> >> > Thanks a lot
> >> > francesco pietra
> >> >
> >> >
> >> > On Tue, Sep 10, 2013 at 4:13 PM, Carlos Simmerling <
> >> > carlos.simmerling.gmail.com> wrote:
> >> >
> >> > > I tend to agree- to my knowledge, this has never been carried out to
> >> > > reasonable convergence in the literature for a peptide this size in
> >> > > explicit water. By "convergence" I mean showing that very similar
> >> results
> >> > > are obtained regardless of starting conformation. That's stricter
> >>than
> >> some
> >> > > reports where it is claimed that the populations are no longer
> >> changing,
> >> > > which I find not as satisfying as it should be (in my opinion).
> >>Niel is
> >> > > right, if you want to just do a conformational search, this could be
> >> fine,
> >> > > but if you're looking for the populations themselves to be reliable,
> >> it's
> >> > > still perhaps intractable.
> >> > >
> >> > > I'm not sure which comments of mine on implicit solvent you
> >>reference.
> >> our
> >> > > GB models have gotten better, and with igb=8 you might find that you
> >> get
> >> > > what you need. Look at our article on it and see if it's what you
> >>need,
> >> > > though the test systems are much smaller than what you're proposing.
> >> > >
> >> > > 1. Nguyen, H., Roe, D. and Simmerling, C., ³Improved Generalized
> >> Born
> >> > > Solvent Model Parameters for Protein Simulations², J. Chem.
> >>Theory &
> >> > > Comput., 9, 20202034 (2013) DOI: 10.1021/ct3010485
> >> > >
> >> > >
> >> > >
> >> > > On Tue, Sep 10, 2013 at 10:01 AM, Niel Henriksen
> >><shireham.gmail.com>
> >> > > wrote:
> >> > >
> >> > > > Francesco,
> >> > > >
> >> > > > More than 200 replicas could be a major challenge, especially with
> >> > > explicit
> >> > > > solvent. If you hope to find some plausible folded
> >>conformations, it
> >> > > might
> >> > > > work (i don't know that you need to go to 600K though). If you
> >>hope
> >> to
> >> > > > converge the entire ensemble, you might want to avoid this
> >>particular
> >> > > > route. I had trouble converging a tetranucleotide in explicit
> >>water
> >> with
> >> > > > ~4 microseconds/replica of simulation (24 replicas).
> >> > > > http://www.ncbi.nlm.nih.gov/pubmed/23477537
> >> > > >
> >> > > > --Niel
> >> > > >
> >> > > >
> >> > > > On Tue, Sep 10, 2013 at 6:45 AM, Francesco Pietra <
> >> chiendarret.gmail.com
> >> > > > >wrote:
> >> > > >
> >> > > > > >Assuming that I am interpreting your question correctly,
> >> > > > >
> >> > > > > Yes, and the answer is very useful: I can assume a larger delta
> >>T
> >> than
> >> > > > the
> >> > > > > 0.8K I reported. Provided that I will be able to calculate the
> >> exchange
> >> > > > > frequency (so far unclear to me how; I can just change the
> >>number
> >> of
> >> > > > > steps/run, I used 100, if increased to 1000 there is no more any
> >> > > > exchange).
> >> > > > >
> >> > > > > At any event, are >200 replicas (as needed with my system for
> >> > > 314-600K) a
> >> > > > > reasonable prospect or one that is destined to result as
> >> technically
> >> > > > > unfeasible? The literature is abundant of variants on small
> >> peptides.
> >> > > > >
> >> > > > > Finally, is exhaustive MD equilibration an absolute need or it
> >>can
> >> just
> >> > > > > help? So far I have not insisted in the equilibration at 314K
> >> > > > (rmsd/frame
> >> > > > > is still raising because - I suppose - of the flexibility of the
> >> > > portion
> >> > > > to
> >> > > > > model: clearly there are low energy barriers)
> >> > > > >
> >> > > > > Thanks
> >> > > > >
> >> > > > > francesco pietra
> >> > > > >
> >> > > > >
> >> > > > > On Tue, Sep 10, 2013 at 1:12 PM, Jason Swails <
> >> jason.swails.gmail.com
> >> > > > > >wrote:
> >> > > > >
> >> > > > > > On Tue, Sep 10, 2013 at 3:38 AM, Francesco Pietra <
> >> > > > chiendarret.gmail.com
> >> > > > > > >wrote:
> >> > > > > >
> >> > > > > > > Hello:
> >> > > > > > > I am progressing toward a major task of carrying out a pure
> >> T-remd
> >> > > > > > > (parallel tempering) with a 34aa peptide in explicit water
> >>for
> >> a
> >> > > > > 314-600K
> >> > > > > > > range. After C. Simmerling reports about implic media, I did
> >> not
> >> > > > > attempt
> >> > > > > > > any simulation under implicit media.
> >> > > > > > >
> >> > > > > > > I started with 8 replicas and geom progressing temp,
> >>noticing,
> >> for
> >> > > > the
> >> > > > > > > 314-320K range, full exchange is obtained. deltaT is 0.8K.
> >> > > > > > >
> >> > > > > > > On increasing the nr of replicas and delta T on the above
> >> basis,
> >> > > thus
> >> > > > > 16
> >> > > > > > > replicas for 314-326K, the exchange is no more so good. That
> >> is,
> >> > > the
> >> > > > > > > highest and the lowest temp do not exchange with one another
> >> > > > directly.
> >> > > > > > >
> >> > > > > > > My question is, do, for example, exchange of 16 with 15
> >>only,
> >> and
> >> > > > > > exchange
> >> > > > > > > of 14 with 15, compensate? In other words, do "local
> >>exchanges"
> >> > > > > > propagate?
> >> > > > > > >
> >> > > > > > > In this affair, I restrained the dihedrals for a two
> >>(starting)
> >> > > alpha
> >> > > > > > > helical turns, which are well defined by X-ray diffraction.
> >>The
> >> > > rest
> >> > > > of
> >> > > > > > the
> >> > > > > > > peptide does not clearly diffract at 100K, and I am
> >>attempting
> >> to
> >> > > > > > simulate
> >> > > > > > > how the conformation, or prevailing cluster of
> >>conformations,
> >> > > should
> >> > > > > be.
> >> > > > > > I
> >> > > > > > > did not apply any other restraint to this undefined part.
> >> Should
> >> > > the
> >> > > > > > > chirality at the peptide bond be imposed even if the
> >>prevailing
> >> > > > > > > conformation is unknown?
> >> > > > > > >
> >> > > > > > > Thanks so much for advice
> >> > > > > > >
> >> > > > > >
> >> > > > > > Assuming that I am interpreting your question correctly, there
> >> is no
> >> > > > need
> >> > > > > > to achieve exchanges between the first and last temperature
> >> replica.
> >> > > > In
> >> > > > > > fact, if you are achieving exchanges between those two a high
> >> > > > percentage
> >> > > > > of
> >> > > > > > the time, then all of the replicas in between are unnecessary
> >> :). As
> >> > > > > long
> >> > > > > > as adjacent replicas exchange frequently enough (about 20% of
> >>the
> >> > > time
> >> > > > is
> >> > > > > > good in my experience), then you will get good enough mixing
> >>in
> >> state
> >> > > > > space
> >> > > > > > to make efficient use of REMD. (Replicas will be able to
> >>diffuse
> >> > > > through
> >> > > > > > state space from the lowest temperature to the highest
> >>_through_
> >> the
> >> > > > > > intermediate temperatures).
> >> > > > > >
> >> > > > > > The following website will give you a good set of starting
> >> > > temperatures
> >> > > > > > between two replicas: http://folding.bmc.uu.se/remd/ (the NPT
> >> > > results
> >> > > > > are
> >> > > > > > good enough for the NVT REMD that Amber runs). It may be
> >>worth
> >> > > > running a
> >> > > > > > quick simulation to verify that all exchange rates are
> >> approximately
> >> > > > what
> >> > > > > > you want them to be before starting major production.
> >> > > > > >
> >> > > > > > HTH,
> >> > > > > > Jason
> >> > > > > >
> >> > > > > > --
> >> > > > > > Jason M. Swails
> >> > > > > > BioMaPS,
> >> > > > > > Rutgers University
> >> > > > > > Postdoctoral Researcher
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Received on Wed Sep 11 2013 - 07:30:03 PDT
