From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Jan 22 2009 - 11:52:29 CST
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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