From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jan 16 2015 - 11:04:44 CST
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.
On Wed, Jan 14, 2015 at 11:07 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> OK, send me input files off-list and I'll look into it.
> 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
>> On Jan 13, 2015, at 7:31 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> 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.
> 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
-- 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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