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

From: sruthi c k (
Date: Thu Jan 07 2016 - 04:31:11 CST

Hi Jerome,
Thank you very much for the quick reply
Best Regards

On Thu, Jan 7, 2016 at 3:40 PM, sruthi c k <> wrote:

> Thank you very much for the quick reply
> On Thu, Jan 7, 2016 at 3:37 PM, Jérôme Hénin <> wrote:
>> 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.
>> Best,
>> Jerome
>> 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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