From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Mar 22 2011 - 17:16:54 CDT
Giacomo,
Sorry because a question on CVS version, but I try to combine GBIS and
ABF (linux CVS-2011-03-20 for Linux-x86_64), and likely that bug exist.
Simulation works when GBIS without ABF are applied, also when GBIS is
excluded but ABF applied, simulation works on 2.7 (win), but no on CVS.
In GBIS and ABF combination, or in "ABF alone" on CVS whole calculation
were initialized properly, but after that crash, without any "error
message" in out file
Please let me know are you try with GBIS and ABF combination in some of
CVS. I use two colvars, one of which is distance between centroid
defined on aromatic ring, and some other 'one atom'; second colvar is
also distance defined on 3 atoms of each of two di-phenyl-methyl
moieties that molecule comprise (also I try there to overcome any
symmetry, when centroids are defined,even there is no constraints). BC
was not applied.
Thanks
Branko
On 3/18/2011 2:02 AM, Giacomo Fiorin wrote:
> Sure, for as long as you select solute atoms when defining the
> variable(s).
>
> Giacomo
>
> ---- ----
> Dr. Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science - Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> giacomo.fiorin_at_temple.edu <mailto:giacomo.fiorin_at_temple.edu>
> ---- ----
>
>
>
> On Thu, Mar 17, 2011 at 4:50 PM, Branko <bdrakuli_at_chem.bg.ac.rs
> <mailto:bdrakuli_at_chem.bg.ac.rs>> wrote:
>
> Is ABF can be applied with GBIS in NAMD 2.8, most probably solvent
> model is not limited to water only. Thanks for respond
>
> Branko
>
>
>
>
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