From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Jul 26 2018 - 11:48:07 CDT
Hi,
That is more or less an expected physical effect when the excluded volume
due to LJ repulsion disappears. In principle the soft-core potentials were
introduced to limit this effect (that is, to spread it over a broader range
of lambda and remove the singularity). You can try experimenting with
softer soft-core potentials by increasing the value of alchVdwShiftCoeff
from its default of 5 Å^2. Just note that the risk with too much softening
is to allow atoms of opposite charges to overlap, which leads to an
electrostatic catastrophe (singular Coulomb energy). So the goal is to keep
the barrier high enough that those clashes don't occur as long as the
Coulomb potential is nonzero. If you are using a protocol that separates
the contributions entirely, that is alchElecLambdaStart
>= alchVdwLambdaEnd, then there is no such risk and I suppose anything goes.
Jerome
On Thu, 26 Jul 2018 at 17:46, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> Hello
> With every ligand-receptor FEP that I am carrying out with NAMD2.12, I
> noticed a sudden drop in the /\A values when when approaching lambda = 1.0,
> which seems to me prone to introducing large errors. I understand what
> happens in the system under such conditions, however i wonder whether the
> trend is out of the norm because I am missing some control.
>
> For example, for a ligand-receptor FEP divided into five sectors (in order
> to keep the calculations for each sector within 24hr), the ParseFEP.log for
> the 0.8-1.0 sector (lambda 0.01, 20 windows) reports lambda//\A
> ......................
> ....................
> 0.9000/1.2495
> 0.9100/1.2395
> 0.9200/1.1549
> 0.9300/1.0130
> 0.9400/0.6102
> 0.9500/-0.0087
> 0.9600/-1.8900
> 0.9700/-3.8335
> 0.9800/-6.8530
> 0.9900/-10.5326
> 1.0000/-15.9730
>
> Thanks for advice
> francesco pietra
>
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