yong
--one other thing
I think we doubled up the excluded atom list so that it atom i can exclude
atoms j with j<i . this is because the grid based list builders destroy
the old logic where atoms are processed serially
I should have put the re-build of excluded atom list into leap---BUT leap
should have been written in fortran and be batch oriented instead of
interactive. we really don't need a fancy compsci solution to the basic
problem of building prmtop and inpcrd files. we need something that all
the developers can easily understand and work with
there's my rant for the week
td
On Fri, 11 Nov 2005, Yong Duan wrote:
>
> Sorry, my message was not clear. I was rather surprised myself. Yes, I
> meant
> sander actually ignores the excluded atom list and re-builds it,
> apparently
> from bond, angle and dihedral lists. I think this is done when extra
> points
> are turned on. Looks like the LES code is gone when you turn on extra
> points
> (hopefully, nobody has tried this combination yet). I think the code was
> changed since amber 7. I am pretty sure the exluded list was used in
> amber5/6. Yes, GB code deals with this "correctly".
>
> I can understand the need to change the excluded atom list with extra
> points. But I thought it should be done in things like Leap, perhaps add
> an
> extra line in prep file to indicate which part is special and needs to
> be
> dealt with in Leap. Minor modification within sander targeted
> exclusively to
> extra points is understandable (and perhaps acceptable). Now, it
> actually
> affects the whole excluded list logic. This seems a bit unusual.
>
>
> yong
>
> -----Original Message-----
> From: owner-amber-developers.scripps.edu
> [mailto:owner-amber-developers.scripps.edu] On Behalf Of Carlos
> Simmerling
> Sent: Thursday, November 10, 2005 5:43 PM
> To: amber-developers.scripps.edu
> Subject: Re: amber-developers: Excluded list ?
>
>
> 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
