AMBER Archive (2005)

Subject: Re: AMBER: convert one functional group to another with TI

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 23 2005 - 16:46:55 CST

On Tue, Feb 22, 2005, Eric Hu wrote:

> Ok, I perturbed one molecule to another which lacks by
> a hydroxide only. I am thinking maybe I should
> calculate the energy difference by perturbing both
> molecules to nothing to prevent such big dV/dL values.

That should not be necessary.

> R M S F L U C T U A T I O N S
> DV/DL = 54.2857
> ------------------------------------------------------------------------------
> DV/DL, AVERAGES OVER 500000 STEPS
>
>
> NSTEP = 1000000 TIME(PS) = 1020.000 TEMP(K) =
> 0.00 PRESS = 0.0
> Etot = 0.0000 EKtot = 0.0000 EPtot = 1465.4880
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 883.5451 VDWAALS = 0.0000
> EELEC = 581.9429 EHBOND = 0.0000 RESTRAINT = 0.0000
> Ewald error estimate: -0.1636E-04
>

It's not at all clear why the DV/DL values are so high; I would try a vacuum
simulation at the same lambda to see if that helps. Do you have close
intramolecular interactions with the OH group that you are changing?

You should certainly try to decouple the electrostatic and atom-type changes
if you are not already doing so. (The output snippet from above shows only
electrostatic changes, so maybe that is already a problem.)

...dac

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