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
>
_______________________________________________
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 Tue May 29 2018 - 08:30:03 PDT
