Re: Regarding merging of .grad files obtained from ABF simulations

From: Jérôme Hénin (
Date: Thu Jan 07 2016 - 04:07:17 CST

Hi Sruthi,

If the ranges are non-overlapping, it is indeed merely a matter of
concatenating the data, and you can easily do it manually. If the ranges do
overlap, then, the accumulated averages are combined, weighted by their
respective sample counts, and the counts are summed.


On 7 January 2016 at 08:49, sruthi c k <> wrote:

> Dear NAMD developers,
> I want to do ABF simulations for getting the free energy profile with
> respect radius of gyration of protein. I have read about dividing the range
> of colvar values into windows and performing ABF simulation in each window
> independently and finally merging the average force files.
> How the merging .grad files obtained from ABF simulations are done in
> NAMD ? I know of including the option inputPrefix in the abf block of
> colvar input file and running NAMD by changing the no of md steps to 0. I
> am interested to know how NAMD does this merging. Is it just a catenation
> of the files or is there any other thing to be taken care of?
> Thanks in advance
> Sruthi

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