From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Jan 17 2015 - 15:34:43 CST
Wonderful - thanks guys!!!
JC
On Jan 16, 2015, at 5:57 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> 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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