On Mon, Feb 13, 2012, Peter Eastman wrote:
>
> First, the AmberTools manual says there are two "flexible water models",
> SPC/Fw and qSPC/Fw. Does that mean that all other water models are
> always rigid, regardless of the value of the ntc flag? If so, how do I
> recognize water moleces in the prmtop file that should be made rigid?
> Or is water actually made rigid or flexible based on the value of ntc,
> just like everything else?
SPC/Fw and qSPC/Fw are *intended* to be flexible; all the others are intended
to be rigid (as far as I know). But what the code actually does depends on
the value of ntc. So, you can make a run with a flexible TIP3P model, but
that would not be desirable. So your final sentence is correct: it's the
value of ntc that counts.
>
> Comparing the frcmod files for the "rigid" and "flexible" water models,
> there's only two obvious differences: the flexible ones include an angle
> term, and the force constant of the H-H "bond" is 0. Presumably those
> differences somehow encode the fact that water should be left flexible,
> but how? Do bonds with force constants of 0 not get constrained with
> ntc > 1? Or does the presence of the angle term somehow tell AMBER
> not to constrain the H-H distance, even though this is water and would
> otherwise be rigid? Or something else?
All bonds that include a hydrogen are fixed if ntc>0. So the water is
rigid because all three bonds are constrained. LEaP actually removes all
of the H-O-H angles (unless you request a flexible water), because they
are not needed. I think it's possible to tell LEaP you have a rigid water
(the default behavior), and then try to run without constraining the water
bonds; that would yield terrible behavior, but I can't remember if we have
any checks to prevent it from happening. (You could try some experiments
along these lines.) Again, it's only ntc that determines the behavior, not
the presence or absence of force constants, etc.
>
> Then there's the frcmod files for TIP4P, TIP4P-Ew, and TIP5P. I don't
> understand those at all. The only bond they define for the extra
> sites is to the oxygen, which obviously isn't enough to define their
> positions. Looking through the source code, it appears that any atom
> whose name starts with EP or LP gets treated in a special way, but I
> don't understand the details. How do I determine the locations for
> these sites?
You are going to have to grok the extra-points code: look at the
define_frames() routine in extra_pts.f. It's moderately(!) well-commented,
and there are special sections for TIP4P and TIP5P water that are clearly
identified. At every step, the location of extra-points are determined by the
position of the nearby heavy atoms.
...hope this helps....dac
--
================================================================
David A. Case | case.biomaps.rutgers.edu
BioMaPS Institute and Dept. of |
Chemistry & Chemical Biology | fax: +1-732-445-4320
Rutgers University | office: +1-848-445-5885
174 Frelinghuysen Road, Rm. 208a | cell: +1-609-651-6817
Piscataway, NJ 08854 USA | http://casegroup.rutgers.edu
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Received on Mon Feb 13 2012 - 13:30:02 PST
