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


From: Amir Hossein Saeedi <asaeedi@...7272...>
Date: Tue, 12 Dec 2017 07:48:39 +0000

You're right!


Honestly, I'm seeking an illustrative tutorial to learn umbrella sampling in lammps, similar to that offered by GROMACS. 

 

Thanks for your helpful link.


If there are any other links, please let me know.



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
Tel: +98 21 82883350
Fax: +98 21 82883350



From: Giacomo Fiorin <giacomo.fiorin@...24...>
Sent: Monday, December 11, 2017 9:43 AM
To: Amir Hossein Saeedi
Cc: lammps-users@lists.sourceforge.net
Subject: Re: [lammps-users] Umbrella Sampling
 
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