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Re: [lammps-users] Umbrella Sampling
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Re: [lammps-users] Umbrella Sampling


From: Giacomo Fiorin <giacomo.fiorin@...24...>
Date: Mon, 11 Dec 2017 16:43:37 -0500

Hi Amir, umbrella sampling is a general free energy calculation technique, which can be applied to a variety of reaction coordinates problems.  I presume you refer to the GROMACS tutorial where the two ends of a peptide are pulled: is that what you are trying to do?

If so, a similar approach in LAMMPS uses the Colvars module.  If you have carried out the necessary steps to set up and equilibrate a system in LAMMPS, use the example here, which is for a steered MD protocol:
http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvars_crash_course

You will need to adapt the atom selections, of course.  Once everything is working for you, you will prepare multiple starting configurations and use a fixed harmonic restraint on each one to run umbrella sampling.

Giacomo


On Mon, Dec 11, 2017 at 2:48 PM, Amir Hossein Saeedi via lammps-users <lammps-users@...396...sourceforge.net> wrote:

Dear Lammps users


Could anybody introduce me a note or tutorial to learn how to conduct "Umbrella Sampling" in lammps?


This process seems to be easy in GROMACS, however, I could not find proper cases for lammps.




With Kind Regards

Saeedi Dehaghani Amir Hossein
Assistant Professor 
Department of Petroleum Engineering
Faculty of Chemical Engineering
Tarbiat Modares University
Address: Tarbiat Modares University, Jalal Ale Ahmad Highway, Gisha Bridge, Tehran, Iran
Mob: +98-9122892230

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--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD