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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Received on Fri Apr 13 2018 - 04:30:02 PDT
