AMBER Archive (2003)

Subject: Re: 10-12 H-bond terms

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Mon May 12 2003 - 14:50:40 CDT

Hi,

Thank you for your reply.

On Sun, 11 May 2003, Andreas Svrcek-Seiler wrote:

>
> > 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 "ridigBonds" option in NAMD has three values none, water and all.
Indeed "all" means all bonds between each hydrogen and the corresponding
mother atom are fixed. I've tried both "water" and "all" thinking that by
using the latter value (all) I might get around with the 10-12 H-bond
term.

> > 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).

I forgot to mention that I use the SPC/E water model but all water models
in amber are parametrized as 3-bond rather than 2-bonds and an angle so
I assume that the above holds for it. I found your e-mail in the archive
and I will give it a try. Thank you!

> 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.

My energies are indeed a bit different but I was more concerned at this
point with the bond energy. Moreover, I've tried to use in amber a larger
cutoff than 6.5 but for a "cut = 8.5A" I've got the following error
message (skinnb=2A by default and as I understand from the manual one
should not change easily the default value)

 Ewald PARAMETER RANGE CHECKING:
parameter skinnb+cutoffnb: (nonbond list cut) has value 0.10500E+02
This is outside the legal range
Lower limit: 0.00000E+00
Upper limit: 0.89703E+01
Check ew_legal.h

Anyhow thanks for pointing it out to me!

Ioana