Re: Abf force output

From: Jérôme Hénin (
Date: Wed Feb 09 2011 - 07:30:16 CST

I meant just one new simulation for all windows.

On 9 February 2011 11:12, stefhoor <> wrote:
> 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:37 CST