AMBER Archive (2003)

Subject: Re: 10-12 H-bond terms

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Sat May 10 2003 - 18:13:08 CDT

Hi,
 

> I used SHAKE thus the bond energy should be zero (which it is in amber).
> However in NAMD this energy (although I use the same condition rigidBonds
> all) is non zero.
I *believe* "rigidBonds all" doesn't mean that all bonds are
SHAKEN/RATTLED in namd, just all bonds involving hydrogens.
> The only thing that draw my attention was a Warning in
> the NAMD output file
> Warning: Encounter 10-12 H-bond term
> Warning: Found 216 H-H bonds.
I again *believe* that's the TIP3P H-H bond. This is ignored in namd.
If you want 'AMBER like' rigid TIP3P water in namd, you could use a trick
I posted here some time ago ( to get the HOH angle constrained as namd
expects).
Besides, it seems that you've turned switching on in your namd command
file. Since AMBER has no switching, this is bound to influence your
non-bondend energy terms. In Addition, a cutoff of 6.5
seems a bit short, but has nothing todo with youe questions.
I don't know how exactly namd handles switching but
if is were done the 'naive' way, a switchdist of 6.0 with a cutoff
of 6.5 would produce ENORMOUS force artifacts for interatromic distances
between 6 and 6.5 A.
That's just my two cents, be sure to consult the namd manual,
as well als probably the namd sources.
Good Luck
Andreas 

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