VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Feb 01 2017 - 08:43:26 CST

Hi Stefano, besides the obvious issue that the metadynamics potential
converges to the negative of the PMF, can you try using the cv save command
in VMD, to write a PMF file?

This file could then be compared to the one written by NAMD (which you
already have), and detect any inconsistencies.

Giacomo

On Tue, Jan 31, 2017 at 9:02 PM, Stefano Guglielmo <
stefano.guglielmo_at_unito.it> wrote:

> Hi all,
>
> For sure I am missing something but I've got a bit confused about the
> discrepancy between the pmf minimum obtained from a metadynamics simulation
> (ie the colvars values corresponding to 0) and the minimum value of
> metadynamics potential calculated for the same simulation through vmd
> colvars module, corresponding to quite different values of colvars compared
> to the previous ones.
> Can anybody give some hints or references?
>
> Thanks in advance
>
> Stefano
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707678
>
>