Hi All ,
see my comments below:
On May 25, 2009, at 11:22 AM, David A. Case wrote:
> On Thu, May 21, 2009, Mark Williamson wrote:
>>
>> My question is, what happens when k is atom one in the system and
>> it needs
>> to be flagged to ignore its 1-4 contribution, e.g. :
>>
>> Given a dihedral of atom index: 4-3-1-7
>>
>> it becomes the prmtop'ed form of: 9 6
>> 0 18
>>
>>
>> Here in lies the problem, you cannot put a sign on a zero:
>>
>> 9 6 -0 18
>>
>
> Just some comments:
>
> 1. Changing the format of the prmtop file would be so onerous, that
> we would
> need a better reason than this one to do that.
>
> 2. Since the entries in the atom list are always divisible by three,
> something
> like "-1" should never appear. So, we could special-case that, so
> that it
> would be treated with the same logical meaning as "-0" ought to
> have. This
> avoids having to do the string manipulations that Gustavo suggested,
> and
> has a doesn't break *backwards* compatibility (since current prmtops
> don't
> have such entries). It is in effect, however, a format change for the
> prmtops, so see item #1 above.
>
> 3. Is there someway to re-order the dihedrals to avoid the problem?
> My
> understanding is that k is negative when there is a previous
> diehdral that did
> the 1-4 interactions, so could some reorganization of the list avoid
> the need
> for "-0"?
Sleap will automatically re-order the dihedrals in such cases (Another
reason to
switch to sleap!)
However, improper dihedral can not be re-ordered since the 3rd atom is
the central
atom.
>
> 4. Alternatively, is it feasible to make the fourth atom index
> negative, rather
> than the third one? [or vice-versa if atom 4 is negative.] The key
> line seems
> to be line 894 in ene.f:
>
> if (k3t < 0 .or. l3t < 0) cycle
>
> So, we might have some wiggle room about changing whether k3t or l3t
> is
> negative, and salvage things that way.
AFAIK, a negative 4th atom indicates an improper dihedrals. Is there
any
special treatment for improper dihedrals?
>
> ...dac
>
>
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Received on Tue May 26 2009 - 01:11:11 PDT
