On Tue, Jan 3, 2012 at 11:09 PM, Geoff Hutchison
wrote:
> On Jan 3, 2012, at 2:45 PM, David Lonie wrote:
>> beyond the trust radius. I didn't track down which is happening, but
>> switching to the Newton2Num line-search method fixes the problem for
>> me (see OBForceField::SetLineSearchType()).
>
On 4 January 2012 12:53, David Lonie wrote:
> On Tue, Jan 3, 2012 at 11:09 PM, Geoff Hutchison
> wrote:
>> On Jan 3, 2012, at 2:45 PM, David Lonie wrote:
>>> beyond the trust radius. I didn't track down which is happening, but
>>> switching to the Newton2Num line-search method fixes the problem f
On Wed, Jan 4, 2012 at 8:47 AM, Noel O'Boyle wrote:
> On 4 January 2012 12:53, David Lonie wrote:
>> On Tue, Jan 3, 2012 at 11:09 PM, Geoff Hutchison
>> wrote:
>>> On Jan 3, 2012, at 2:45 PM, David Lonie wrote:
beyond the trust radius. I didn't track down which is happening, but
switch
On Jan 4, 2012, at 9:19 AM, David Lonie wrote:
> If there is an easily parsed / imported / OBConv-ertable database of
> structures somewhere, it wouldn't be too difficult to come up with a
> test.
I think the question would be "how many molecules do you want?" There's a set
of 18 molecules in t
On Wed, Jan 4, 2012 at 11:04 AM, Geoffrey Hutchison
wrote:
> On Jan 4, 2012, at 9:19 AM, David Lonie wrote:
>> If there is an easily parsed / imported / OBConv-ertable database of
>> structures somewhere, it wouldn't be too difficult to come up with a
>> test.
>
> I think the question would be "ho
Dear Prof. Hutchison,
Yes, thats what I want to do.
I followed your suggestions, at least as far as I understood it.
1. I built a new side chain w/ 3D coordinates from OBBuilder (stored as OBMol
newSideChain)
2. Deleted the required sidechain atoms from the origMol.
3. Added all the atoms of n
Long email ahead, but here is my implementation of BFGS and L-BFGS in
Python from one of my research code, if anyone is interested in going
down that route:
https://gist.github.com/1561144
but see my comment about why neither of these may be the right thing.
-
>>> Other important factors to tes
On Wed, Jan 4, 2012 at 12:48 PM, Jiahao Chen wrote:
> Long email ahead, but here is my implementation of BFGS and L-BFGS in
> Python from one of my research code, if anyone is interested in going
> down that route:
>
> https://gist.github.com/1561144
This is a good summary of various line search
