Re: Running bias exchange metadynamics simulations with NAMD

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Sun Jan 02 2011 - 15:03:48 CST

I have another question, which is in essence:
what are the differences between bias-exchange metadynamics and the multiple
walkers method?

If I would just run multiple replicas using NAMD, each replica with it's own
CV bias, isn't this almost a bias exchange method?
Or must all the replicas share the same CVs? This part of the documentation
seems to suggest that all the CVs must be the same:
"*Note: **multidimensional PMFs can only be obtained with one
*metadynamics* instance
applied to all the colvars, and not with multiple instances each applied to
a single colvar*."
But I'm not 100% sure I understood this correctly. (also, must the potential
of the bias for all replicas also be the same?)

Best regards,
Ajasja Ljubetič

On Sat, Jan 1, 2011 at 22:48, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:

> Dear Ajasja,
>
> 2010/12/30 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>:
> > Dear all,
> > The bias exchange metadynamics is very reminiscent of the replica
> exchange
> > method. Since the latter is implemented as a set of TCL scripts, would it
> > be feasible to implement bias exchange in the same way? (ie Does one have
> to
> > restart NAMD in order to change the colvar biases?).
>
> At this point, yes, you would have to restart NAMD.
>
> Best,
> Jerome
>

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