From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Feb 15 2012 - 13:48:50 CST
Hello Simone, the RMSD is with respect to one structure. You provide this
structure via e.g. a PDB file, define the atoms to be fitted onto it, and
the RMSD will be computed at every time step, on the same atoms. If you
need two structures (start and end), you can either define two RMSDs, or
use a combination of the two values.
Searching the mailing list archives a bit more may have provided this
thread from less than two weeks ago:
where each of the answers can certainly help you.
The message referred to ABF, but the difference with metadynamics is just
using "metadynamics" instead of "abf". My general advice is, search for
answers and/or example regarding a specific variable, because most of the
times you can use on it any method you want. So searching for
"metadynamics", "abf" or any other method will only narrow down your
There is an example of input file, right in the relevant section of the
NAMD user's guide:
The example is to apply an harmonic restraint to a couple of distance
To adapt it to one of the 17 other types of variables, as I said try to
search for that variable type first. Once you defined your variable,
applying metadynamics or one of the other methods is pretty straightforward.
On Wed, Feb 15, 2012 at 2:25 PM, simone bardwell <sbard79_at_gmail.com> wrote:
> I have a couple of questions regarding setting up
> metadynamics calculations in NAMD. I have looked though the archive user
> list but have not found a response to my questions.
> I would like to use RMSD as a CV for a metadynamics calculation. I would
> like to be able to specify a start and end structure and then a set of
> atoms to use to fit the structures together and then measure the rmsd of a
> different region. I have read the Manual however am not sure if the region
> being specified is for the fit and will also be the region to measure.
> My second question is whether anyone has any practical examples of RMSD
> metadynamics input files they would be willing to share. I have searched
> for tutorial examples for these types of calculations however with no
> success. To be able to refer to an example would be really helpful.
> Kind regards,
> Simone Bardwell
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