[gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs

[Erik Marklund]

Hi,

Just out of curiosity, what is the point of REMD for such a simple system? Is the enhanced sampling really worth the overhead?

Kind regards,
Erik
______________________________________________
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 9 Mar 2018, at 18:43, Marc Hoemberger <hoemberg at brandeis.edu<mailto:hoemberg at brandeis.edu>> wrote:

You could compile Gromacs with PLUMED (http://www.plumed.org/)  and use
that to run your umbrella sampling with replica exchange.

-Marc

On Thu, Mar 8, 2018 at 11:32 AM, Mayank Dixit <dixit.mayank2 at gmail.com<mailto:dixit.mayank2 at gmail.com>>
wrote:

Dear Gromacs Users,
I would like to calculate the potential of mean force between sodium and
chloride ion pair in water using replica exchange umbrella sampling method
in gromacs. Please let me know the details of replica exchange umbrella
sampling in gromacs.

Thanks and kind regards
Mayank

​


*Dr. Mayank  Dixit *
Post-doctoral fellow
Department of Chemistry
The city college of New York
Marshak Science Building
160 convent avenue 138th street.
New York, NY-10031
Cell no: 16465894905
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Marc Hoemberger
Ph.D. Candidate, Biochemistry and Biophysics,
Laboratory of Dorothee Kern
MS-009, 415 South St.
Brandeis University
Waltham, MA, 02453
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