LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] run metadynamics using Users-COLVARS
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] run metadynamics using Users-COLVARS

From: liyi bai <liyibai2011@...24...>
Date: Wed, 13 Dec 2017 01:19:53 +0900

liyi bai

签名由 网易邮箱大师 定制

On 12/13/2017 00:32, Giacomo Fiorin wrote:
Hi Liyi, you cannot specify a "region" in the sense of the LAMMPS commands that dynamically selects atoms, because the appearing and disappearing at the region's boundaries would make the collective variable discontinuous.  You can, however, define a "group" with the atoms of interest and for example study the PMF of displacement along the vertical axis of your problem.  (Beware that the computation may expensive, as it is not fully parallelized: test this for your system).

For your convenience, you can select atoms using Colvars commands or LAMMPS commands and converting back and forth with:

A variable you may want to look at is distanceZ, which supports umbrella sampling, metadynamics, ABF, etc.


On Tue, Dec 12, 2017 at 4:14 AM, liyi bai <liyibai2011@...24...> wrote:
Dear User,

I am wondering if LAMMPS Colvars can specify the particular Volume in simulation system.(As shown in below figure),I would like to know whether it is possible to defined the region of V?

Looking forward to hearing from you.

Thank you very much in advance!

Best Regards


Check out the vibrant tech community on one of the world's most
engaging tech sites,!
lammps-users mailing list

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