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


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

liyi bai
邮箱:liyibai2011@...24...

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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:
http://lammps.sandia.gov/doc/group2ndx.html

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

Giacomo



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

Liyi

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