From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Oct 27 2015 - 15:55:13 CDT
As stated in the previous email, the state file contains a grid with the
metadynamics energy and forces. The energy as a function of the grid's
position is the biasing potential, by definition.
On Tue, Oct 27, 2015 at 3:38 PM, Fidan Sumbul <fidansumbul_at_gmail.com> wrote:
> Dear Dr. Fiorin,
> Thank you for your reply. Sorry for the mistake I ment the second column
> in the traj file as the collective variable.
> Do i have to calculate the biasing potential using these values or is it
> already written in the state file as decribed?
> Fidan Sumbul
> On 27 Oct 2015, at 21:14, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
> Fidan, the first column of the traj file is the step number, the second is
> the collective variable.
> There is no kinetic energy by default in metadynamics.
> The email thread refers to the data found in the state file, which
> contains a grid with the metadynamics energy and forces, and additional
> explicit Gaussian hills when these are off-grid.
> On Tue, Oct 27, 2015 at 2:05 PM, Fidan Sumbul <fidansumbul_at_gmail.com>
>> Dear NAMD Users,
>> I'm trying to perform a multiple replica well-tempered metadynamics
>> simulation by using an eigenvector as bias. As a trial, I perfomed a 20ps
>> run with a 300K temperature increase. The simulation completed without any
>> problem. However, I would like to calculate the biasing potential during
>> the simulation. I know the first column of the colvars.traj file is the
>> value of the bias, but I didn't understand what is the last column
>> (E_metadynamics1) is for. Is it the summation of the E_potential and
>> E-kinetic of the bias?
>> I found a conversation in this mailing list stating that the first list
>> of data after the definition of the colvars is the biasing potential.
>> My second question is, if it is so, shouldn't it be as many as the number
>> of output step as in the colvars.traj file?
>> I'm attaching colvars.state file and colvars.traj file.
>> thank you in advance for your answers.
>> Fidan Sumbul
>> PhD Student and T.A.
>> Polymer Research Center
>> Department of Chemical Engineering
>> Bogazici University
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 http://goo.gl/Q3TBQU http://giacomofiorin.github.io/ https://icms.cst.temple.edu/members.html
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