Hi,
You may also be interested in CreateRemdDirs
(
https://github.com/drroe/CreateRemdDirs), a tool I created a while
back to assist with setting up, launching, and analyzing
multi-dimensional REMD simulations with Amber.
-Dan
On Fri, Apr 13, 2018 at 7:15 AM, Cruzeiro,Vinicius Wilian D
<vwcruzeiro.ufl.edu> wrote:
> Hello Jason,
>
>
> Section 21.5.7 of the AmberTools17 manual talks about Multidimensional REMD. In addition to the groupfile and the mdin files, you will also have to prepare an additional input file used for MultiD-REMD simulations.
>
>
> AmberTools18, to be released soon, will have extended support to Multidimensional REMD. One of the new AmberTools, called genremdinputs.py, was written with the intent to make the process of generating input files for any REMD simulation, including MultiD-REMD, significantly easier. In your case, this tool would automatically prepare the groupfile, mdin files and the MultiD-REMD input file. Instructions on how to use it will be available in the Amber18 manual.
>
>
> I hope this helps,
>
> Best,
>
>
> Vinícius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633
>
> ________________________________
> From: Jason Ku Wang <jwang198.stanford.edu>
> Sent: Friday, April 13, 2018 3:56:17 AM
> To: AMBER Mailing List
> Subject: [AMBER] Two-Dimensional Replica Exchange in AMBER
>
> Hi AMBER Community!
>
> I'm interested in running 2D (multidimensional) replica exchange. In
> particular, I would be interested in exchanging temperatures and
> Hamiltonians.
>
> I've noticed that AMBER has a tutorial for one-dimensional,
> temperature-based replica exchange, but it's unclear how Hamiltonian
> replica exchange and 2D replica exchange are done.
>
> In the following paper https://urldefense.proofpoint.com/v2/url?u=https-3A__pubs.acs.org_doi_abs_10.1021_ct400862&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQBJXyFyocKAWXc&m=_0LqEevXCpoBwsZd6BCdYRQYBiYoa0bwWvxhKH0gv5U&s=nztibXXsDbr3vjdgnHyZNq01G-MqFo0l_jY_7Wto2z0&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pubs.acs.org_doi_abs_10.1021_ct400862k&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQBJXyFyocKAWXc&m=_0LqEevXCpoBwsZd6BCdYRQYBiYoa0bwWvxhKH0gv5U&s=dahfnXEaY2-2iCukzF8VrwbyvHOXSbdasNqkZeVCbb8&e=> by Bergonzo et al., we see
> that temperature-based, Hamiltonian-based, and multidimensional replica
> exchange were implemented in the AMBER.
>
> What would be the best way to run or access code for multidimensional (2D)
> replica exchange on AMBER?
>
> Thanks so much for all your help!
> Jason
> ᐧ
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Apr 13 2018 - 08:00:02 PDT
