I haven't got a chance to use pmemd since I am not accessible to Amber9 now.
I am wondering what value of rgbmax should be safe for the big protein
(25,000 atoms).
Thanks,
Wei
On 5/31/07, David A. Case <case.scripps.edu> wrote:
>
> On Thu, May 31, 2007, Wei Chen wrote:
> >
> >
> > In order to speed up, I have to make cutoff and rgbmax as small as
> possible.
> > >From my single point calculation, I see that a 16 Angstrom cutoff
> should be
> > good. But I am not sure whether I have to use a large value for rgbmax,
> > since there is a difference of 500 kcal/mol between rgbmax=16 and
> > rgbmax=999, which is 1% of total elec. energy. Using large rgbmax really
> > slows down the simulation.
>
> Changing rgbmax changes the physical approximations made in gb theory: the
> effects of long-distance atoms on the local effective radii are ignored.
> You can't tell whether this is good or bad just by looking at the total
> energy. What is important is the way in which the potential energy
> surface is
> changed. And I don't think much is really know about this aspect.
>
> ...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jun 03 2007 - 06:07:29 PDT
