From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Jan 16 2015 - 16:57:58 CST
This fix will be in the Jan 17 nightly build.
Jim
On Fri, 16 Jan 2015, Giacomo Fiorin wrote:
> Hi JC, I found the issue: recently we had changed a couple of things in how
> the atomic coordinates are updated, and the hBond variable was mistakenly
> let behind. My apologies. The alpha variable was affected simply because
> it makes use of hBonds' functions.
>
> I'm sending to you the updated source file, and to Jim for inclusion in the
> next NAMD nightly build.
>
> Giacomo
>
> On Wed, Jan 14, 2015 at 11:07 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> OK, send me input files off-list and I'll look into it.
>>
>> Giacomo
>>
>> On Wed, Jan 14, 2015 at 10:58 AM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>>
>>> Yes, things like distance work, even with drude particles as part of the
>>> groups.
>>>
>>> Thanks!
>>> JC
>>>
>>> On Jan 13, 2015, at 7:31 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>>> wrote:
>>>
>>> Do any other colvars work besides those two?
>>> On Jan 13, 2015 7:09 PM, "JC Gumbart" <gumbart_at_ks.uiuc.edu> wrote:
>>>
>>>> It seems that certain colvars don’t work with the drude force field,
>>>> such as alpha and hbond. Because the alpha colvar might involve drude
>>>> particles, I could see it being a problem, but hbond should only involve
>>>> the two atoms provided? The alpha colvar returns “nan” and hbond is always
>>>> maxed at 1.0.
>>>>
>>>> Any thoughts on how to fix it or deal with it? I tested it in the
>>>> latest NAMD 2.10. I can provide files if needed.
>>>>
>>>> Thanks!
>>>> JC
>>>>
>>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Assistant Professor of Research
>> Institute for Computational Molecular Science (ICMS)
>> College of Science and Technology, Temple University
>> 1925 North 12th Street (035-07), Room 704D
>> Philadelphia, PA 19122-1801
>> Phone: +1-215-204-4213
>> https://icms.cst.temple.edu/members.html
>> http://giacomofiorin.github.io/
>>
>>
>
>
> --
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
> https://icms.cst.temple.edu/members.html
> http://giacomofiorin.github.io/
>
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