From: Dr. Eddie (eackad_at_gmail.com)
Date: Fri Mar 11 2016 - 09:35:03 CST
Thanks Norman, that does make sense. So do most REMDs use some implicit
solvent? I should specify this is not for folding/unfolding. I can't find
anything about solvent in the tutorial or example so thank you very much
for your help.
Eddie
On Thu, Mar 10, 2016 at 4:53 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Using explicit solvent is possible, but cause of the required potential
> energy histogram overlap of neighbored replicas, you need lots of replicas
> as the energy differences between temperatures are too high to reach a
> reasonable exchange probability otherwise. There are improved algorithms
> which address this issue e.g. TIGER2 – Temperature Intervals with Global
> Exchange of Replicas.
>
>
>
> Using npt is technically possible, but you need to implement a way to
> compute a suitable target pressure at each temperature. On the other hand,
> there’s a problem with proving the balanced condition with npt, since it
> changes the dimensions in conformational space and so can’t be proven to
> produce a boltzman weigthed sampling, which as I understood generally
> means, than you can’t know if the folding pathway your REMD takes, can
> happen in reality the same way.
>
>
>
> Norman Geist
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Dr. Eddie
> *Gesendet:* Donnerstag, 10. März 2016 19:26
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* Re: namd-l: Tutorial example of replica exchange
>
>
>
> Thanks Josh. However, now this has raised another question: can you
> perform a REMD with explicit solvent?
>
>
>
> If you don't have PBC and you heat to 600k won't the water just evaporate
> away. Even if the sample was not heated that much couldn't the protein
> reach the surface of the water sphere?
>
> Sorry for all the questions, but that you for your help!
>
> Eddie
>
>
>
> On Thu, Mar 10, 2016 at 10:04 AM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
>
> Hi Eddie,
>
> I don't think there is. The way I like to think about replica exchange
> methods is that you are running N parallel simulations that happen to be in
> communication. Just because two replicas exchange temperature/biases, it
> doesn't prevent each simulation from being its own continuous simulation
> (albeit one where the conditions keep changing). In this way the periodic
> boxes don't swap between simulation, and whatever barostat you picked will
> still try its darndest to keep the replica at the set pressure.
>
> -Josh
>
>
>
> On 03/10/2016 09:46 AM, Dr. Eddie wrote:
>
> Thank you Norman, that helps!
>
>
>
> For anyone else who had the same/similar problem I solved it by compiling
> Namd (2.11) from source and got it working with mpi (not CUDA) with the
> steps above. All multicore binaries (w/wo cuda) failed with those errors
> (see above).
>
>
>
> Now that it runs, I cannot find any information on periodic BC or using a
> Piston with REMD. Is there some limitation?
>
> Thanks,
>
> Eddie
>
>
>
> On Thu, Mar 10, 2016 at 2:03 AM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
> Hey,
>
>
>
> 1) The jobX.conf will just put together the *_base.namd the
> *_remd.namd and and will source the replica.namd script which actually does
> the REMD. Also it is used to source additional restart.files from job1 and
> higher. You will get output files named like the job. So it’s just some
> kind of output separation if you want to restart the simulation multiple
> times.
>
> 2) Shouldn’t you specify how many processes to launch or threads to
> use? Otherwise try to use a non GPU version an see if it helps. There’s
> seems to be a problem with CUDA REMD, especially when using GBIS.
>
>
>
> Let us know
>
>
>
> Norman Geist
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Dr. Eddie
> *Gesendet:* Dienstag, 8. März 2016 23:56
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: Tutorial example of replica exchange
>
>
>
> Hi all,
>
> I am trying to learn how to REMD with namd 2.11 by following the (spartan)
> tutorial
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_namd_2.11_ug_node69.html&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=0tR0d-bxwpiIUv6mbDGaj1Wr4Hu_Mwp3MMx8x1Imbjs&s=K4ShHOBc3RHhIQu07hNgw172edRLwiuO7S4_Ur-6y0U&e=>.
> I have two problems:
>
> 1) I don't understand what jobX.conf are doing exactly and why two are
> commands are needed (first job0.conf then job1.conf)
>
> 2) I can't get it to run:
>
> ~/bin/NAMD_2.11_Linux-x86_64-multicore-CUDA/lib/replica/example$ mpirun
> ../../../namd2 +idlepoll +replicas 8 job0.conf +stdout output/%d/job0.%d.log
>
> Charm++: standalone mode (not using charmrun)
>
> Charm++> Running in Multicore mode: 1 threads
>
> --------------------------------------------------------------------------
>
> mpirun noticed that process rank 0 with PID 23811 on node heartofgold
> exited on signal 11 (Segmentation fault).
>
> --------------------------------------------------------------------------
>
>
>
> Nothing comes out so I can't see any errors:
>
>
>
> ~/bin/NAMD_2.11_Linux-x86_64-multicore-CUDA/lib/replica/example$ ls
> output/*
>
> output/0:
>
> total 0
>
>
>
> output/1:
>
> total 0
>
>
>
> output/2:
>
> total 0
>
>
>
> output/3:
>
> total 0
>
>
>
> output/4:
>
> total 0
>
>
>
> output/5:
>
> total 0
>
>
>
> output/6:
>
> total 0
>
>
>
> output/7:
>
> total 0
>
>
>
>
>
> I've tried using +idlepoll since this is a gpu build, but this changed
> nothing. Any help or idea would be most welcome!
>
> Thanks,
>
> Eddie
>
>
>
>
>
> --
>
> Eddie
>
>
>
>
>
>
>
> --
>
> Eddie
>
-- Eddie
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