On 7/26/13 4:06 PM, Quintin Sheridan wrote:
Dear Gromacs Users,
Is it possible to run free energy calculations in parallel using mpirun? If
Yes, the free energy code is parallelized, either via MPI or threads.
not I am wondering what the fastest way to run a free energy calculation
is. I am basing my free energy calculation on the tutorial by Justin Lemkul
found at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html
I am trying to use the Bennet Acceptance Ration method (g_bar) to get the
free energy of solvation for an ionic liquid. I have tried decoupling an
ion pair from the system as well as individual ions. These simulations
will run locally but when I try to run them in parallel I get the error:
Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 2.26125 nm
Consult
http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm.
This topic is discussed frequently, particularly in the context of free energy
simulations, because there are unique factors that come into play in terms of
the DD algorithm. Search the archive and you will surely find the detailed
explanations.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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