Re: how to define the numsteps in ABF or metadynamics simulation?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jul 12 2011 - 15:06:17 CDT

Hi Clark, numsteps refers to the duration of the NAMD job, which you will
most likely restart several times to achieve a long simulation, like you do
with straight MD. You just create ABF.conf or whichever file on top of the
regular MD run.

Regarding the time required to complete an ABF or metadynamics calculation,
the time is "as long as it takes". You have to check that the PMF obtained
are converged and make sense to you.

Giacomo

On Thu, Jul 7, 2011 at 12:08 AM, Clark Zhang <clarkzhy_at_gmail.com> wrote:

> Hi, everyone!
>
> I want to calculate the PMF along a colvar (distance), then I tried to
> perform an ABF and metadynamics simulation. But I am not sure how to define
> the numsteps in the ABF.conf file? How many MD steps should I carry out
> enough to get reasonable PMF? Is there any rules to calculate the parameter
> - "numsteps"? how many should this parameter("numsteps") be at least?
>
>
> --------------
> Clark Zhang
> 2011-07-07
>
>

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