Re: ABF using distance-com but with negative xiMin

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri Jan 11 2008 - 17:19:32 CST

Hi Phil, good to hear from you!

Yes, distance-com is a "real" distance, hence always positive. For
your purpose, I'd suggest zCoord if your pore is aligned along the z
direction. zCoord is an algebraic distance (really the dot product of
a vector and a reference axis).

Let me know how that works for you.
Jerome

On Jan 11, 2008 10:21 AM, Philip Fowler <philip.fowler_at_bioch.ox.ac.uk> wrote:
> Hi,
>
> I am using the adaptive biased forcing method to calculate the
> potential of mean force through a pore. I therefore define abf1 as the
> atoms lining the pore and abf2 as the ion I am moving through the pore.
>
> My problem is that xiMin seems only to be able to take positive values
> even if I set it to be negative which I need in order to move the ion
> all the way along the pore.
>
> (a) Am I correct that xiMin can only be >= 0 for distance-com?
> (b) If so, does anyone have another ABF reaction coordinate Tcl file
> that fixes this
> (c) or does anyone have any other ideas?
>
> Thanks,
>
> --Phil Fowler
>
>

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