From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Thu Jan 22 2009 - 12:56:40 CST
Hi,
I am using
abf xiMin -180.0
abf xiMax 0.0
with a dxi of 5 I have seen this size of sample in other simulations where
they got convergence of the angle.
On Thu, Jan 22, 2009 at 6:52 PM, Jerome Henin <jhenin_at_cmm.chem.upenn.edu>wrote:
> Hi Jorgen,
>
> I recommend running the calculation in two separate windows (say,
> [-180:0] and [0:180]). There are several reasons to do that:
> 1) it's easier to get even sampling in narrower windows
> 2) you can run them in parallel (linear scaling!)
> 3) it avoids the behavior where the angle always rotates in the same
> direction, which gives an asymmetric (and wrong) PMF.
>
> Jerome
>
> On Thu, Jan 22, 2009 at 12:16 PM, Jorgen Simonsen <jorgen589_at_gmail.com>
> wrote:
> > Hi all,
> >
> > I have been using the ABF methods in order to estimate some energy around
> a
> > phi-angle in a peptide with 8 residues. I have applied the following
> > specifications
> >
> > fullSamples 5000
> > dSmooth 0.1
> > forceConst 1.0
> >
> > I have been running the simulation for 12 ns and the distribution is not
> > uniform and some of the gradients are around -0.15. Is there a way to
> speed
> > up convergence - any comments or suggestions appreciated.
> >
> > Thanks in advance
> >
> > Jorgen
> >
>
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