Hi Travis,
The procedure for loading a NetCDF reservoir is the same as loading an
ASCII reservoir. Use the -rremd flag to indicate which type (Boltzmann vs
Non-boltzmann) of reservoir REMD you want to perform and then the
-reservoir flag to indicate the NetCDF reservoir file. Also, you don't need
the -saveene flag, NetCDF reservoirs have the energies in the reservoir
file itself. I see that the manual does not mention how to load NetCDF
reservoirs but it is the same procedure. "createreservoir" command in
cpptraj is the best way to build NetCDF reservoirs.
Yes, the hybrid-solvent model will also be supported soon. We are testing
the code currently.
Best,
Koushik
Simmerling Lab
On Tue, May 29, 2018 at 11:09 AM, Hurst, Travis C (MU-Student) <
tchvw5.mail.missouri.edu> wrote:
> Dear Professor Simmerling,
>
>
> Thank you for your help!
>
>
> After using the createreservoir option to build the reservoir, I was not
> sure what flag to use to load the NetCDF reservoir into memory when
> beginning the R-REMD simulation using sander. After digging through the
> code, I found the reservoir_ncid value should be changed from -1 to read in
> the NetCDF reservoir, but I did not get much farther on that. Once I
> realized that the GPUs are not supported yet, I started working to use some
> of the other methods.
>
>
> That is great that pmemd support is coming soon for R-REMD! Will the
> hybrid solvent model be supported soon as well?
>
>
> Best,
>
>
> Travis
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, May 25, 2018 12:07:02 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Reservoir REMD using GPUs
>
> sorry for the delay in replying. In the current release, R-REMD is only
> supported in sander. We plan to release pmemd support this year as a patch
> to Amber 18. Dan Roe might be able to better answer your questions about
> using the createreservoir command in cpptraj - is this a problem you're
> having with sander, or in the cpptraj part?
>
> The only recent enhanced sampling I have seen for RNA in explicit solvent
> is work from Christina Bergonzo with Tom Cheatham, and the systems are much
> smaller than 20nt. I think that RNA of that size in explicit solvent will
> still be very challenging.
> CS
>
> On Wed, May 16, 2018 at 6:25 PM, Hurst, Travis C (MU-Student) <
> tchvw5.mail.missouri.edu> wrote:
>
> > Hello Everyone,
> >
> >
> > I have been doing some REMD simulations on a small (20 nt) RNA hairpin in
> > explicit solvent using Amber16, which have been going great thanks to the
> > manual and help from the archive. I am using the results from these runs
> to
> > build PMFs for the hairpin.
> >
> >
> > Now, I am interested in using a high temperature structure reservoir to
> > speed up the convergence of the simulations. However, when I try to use
> > pmemd.cuda.MPI to run the simulations, pmemd does not recognize the
> -rremd
> > flag. Is there a way to use GPUs for running R-REMD simulations or is
> > sander.MPI the only option? I have gotten the R-REMD simulation to work
> > using sander.MPI, but mdinfo estimated about 5700 hours to finish, so
> > incorporating the GPUs is definitely necessary for production runs if I
> use
> > this method.
> >
> >
> > Additionally, I found the createreservoir command in the manual and built
> > a structure reservoir using that, but I am not sure how to load this into
> > memory for the R-REMD simulations to properly read the files. I tried
> > placing the name of the reservoir after the -reservoir flag, but the
> > simulation cannot find the files. Before finding the createreservoir
> > command, I built a reservoir by opening cpptraj, reading in the
> > parm/trajectory files, and using trajout ./reserv/frame restart to build
> > the reservoir. Then, I changed the file numbers from the command line to
> > fit the format from the manual. This seems to work ok, but the
> > createreservoir command works faster and uses much less memory.
> >
> >
> > Finally, if anyone has any advice on other enhanced sampling methods that
> > may be more appropriate for rapidly getting accurate PMFs for this
> system,
> > I am all ears.
> >
> >
> > Best,
> >
> >
> > Travis
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu May 31 2018 - 13:00:03 PDT
