|From:||Amir Hossein Saeedi <asaeedi@...7272...>|
|Date:||Tue, 12 Dec 2017 07:48:39 +0000|
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
Department of Petroleum Engineering
Faculty of Chemical Engineering
Tarbiat Modares UniversityAddress: Tarbiat Modares University, Jalal Ale Ahmad Highway, Gisha Bridge, Tehran, Iran
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
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:
On Mon, Dec 11, 2017 at 2:48 PM, Amir Hossein Saeedi via lammps-users <lammps-users@...396...