Here's another problem in 2.3.x that's not in 2.2.x. I realize these are
bogus molecules, but it illustrates a serious problem.
$ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o can
[Fe-2][Fe+2].[Fe-2].[Fe+2]
Everything looks good -- charges are maintained. Now go through the SDF
forma
> To make the OB force fields work with large amounts of atoms,
> the non-bonded pairs should be detected dynamically.
Well, I'm not sure if that's really a performance win. Probably these need to
be *updated* every 10 steps or something.
> force field calculations. I noticed that periodic bound
Hi,
The problem is that all vdw and electrostatic pairs are precomputed in
the current implementation. Setting cut-off values doesn't change
this. To make the OB force fields work with large amounts of atoms,
the non-bonded pairs should be detected dynamically.
Tim
On Wed, May 16, 2012 at 6:17 P
> Isn't there some way to turn down the VdW via a distance cutoff or so?
(EnableCutOff and SetVdWCutoff) I've never used these but hopefully they
will prevent the pairwise generation of all of the VdW terms.
Curiously, this doesn't work. Enabling the cutoffs and setting to very small
values still
> Isn't there some way to turn down the VdW via a distance cutoff or so?
> (EnableCutOff and SetVdWCutoff) I've never used these but hopefully they will
> prevent the pairwise generation of all of the VdW terms.
Yes, exactly.
-Geoff
--
Oops, meant to reply to the list.
That indeed was the problem. Building a list of atoms to remove and
then removing then in a separate loop worked like a charm.
Thanks,
Greg
On Wed, May 16, 2012 at 7:16 AM, Noel O'Boyle wrote:
>
>> Any thoughts on why pybel.formula is not updating when I use
> Any thoughts on why pybel.formula is not updating when I use the
> underlying OBMol.DeleteAtom?
>
This is a FAQ. Don't delete atoms from whether a loop using an Open Babel
iterator as it invalidates the iterator. Instead, just create a list of
OBAtoms, and in a separate loop delete each OBAtom i
I am a new to OpenBabel. I try to compile OpenBabel-2.3.1 with VS2010, But I
get some errors,can somebody help me, thanks in advance.
Error 1:
alias.cpp
D:\MinGW\home\matchcoder\openbabel-2.3.1\src\alias.cpp(75) : error C2001:
newlin
e in constant
D:\MinGW\home\matchcoder\openbabel-2.3.1\src\alias
I don't have any C code but the output is a series of hexadecimal numbers
listed in reverse order (i.e the last number is for the first 32 bits, the
hexadecimal number itself is not backwards or anything). If you read all of
those numbers into a list, and then pass it to a function like pybel's
_fi
Isn't there some way to turn down the VdW via a distance cutoff or so?
(EnableCutOff and SetVdWCutoff) I've never used these but hopefully they
will prevent the pairwise generation of all of the VdW terms.
- Noel
On 15 May 2012 22:40, Tom Daff wrote:
> I work with molecular crystals and was ver
10 matches
Mail list logo
