Hi,
I've fumbled upon the same issue while dealing with coarse-grain
simulations. As far as I understood, the excluded atom list is rebuilt
only when PME is turned on with extra point (perhaps Tom D. knows more
about this). This is done in extra_pts.f, and can be turned off through
chngmask (see comments in extra_pts.f), I think. For GB calculations,
the excluded atom list in prmtop is used.
Regards,
Guanglei
Carlos Simmerling wrote:
> are you saying that sander ignores the exlusion list in the prmtop?
> if so, I think that is not a good idea and should have been widely
> discussed before being done. It would break a few things that
> I have done. Where is that code?
> carlos
>
> Yong Duan wrote:
>
>> Just realized that sander actually re-constitutes the excluded list
from
>> bond, angle, dihedral lists. Any insightful comments why it has to be
>> done
>> this way? What will happen if I disable this (i.e., remove the code)?
>> I need
>> some flexibility in the excluded list but don't like to break too many
>> things :(.
>>
>>
>> yong
>>
>>
>>
Received on Wed Apr 05 2006 - 23:49:50 PDT
