Re: Abf force output

From: stefhoor (
Date: Wed Feb 09 2011 - 04:12:50 CST

So in this case I would have to simulate all the separation path
again? All windows again? Isn't there a rerun option on namd? I mean,
isn't there a way of gathering the system force from the trajectories
I have already calculated?
Thank you

2011/2/9 Jérôme Hénin <>:
> Hi,
> You can make the assumption that the force distribution and
> autocorrelation time are similar across different windows (this is
> certainly true for the distribution - it is more problematic for the
> correlation time). Then, you just need one additional ABF simulation
> where you collect the system force trajectory ; from there you can
> estimate the distribution and autocorrelation time.
> Jerome
> On 9 February 2011 03:58, stefhoor <> wrote:
>> I have performed an ABF calculation by divinding my reaction path into
>> numerous intermediate steps. Each interval (0.4 angstrom wide) with a
>> pull step size of 0.1 A was calculated in a 2 ns window. At the end I
>> gathered everything with a 0 md step configuration file, which gave me
>> an integrated pmf file with my entire path. I needed to make an error
>> analysis of my calculation. I read several papers, most of them were
>> referenced here in namd's mailing list, and got to the conclusion that
>> I need to calculate the instantaneous force by adding the
>> outputSystemForce option within a colvar {} block. Does this mean that
>> I would have to perform all simulations again in order to compute this
>> force or is there a way to get them from my current files?
>> Thank you

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