From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Thu Aug 20 2009 - 09:21:41 CDT
Hi again,
The colvars section for my single dihedral is seemingly OK now. You had
advised me earlier that the ABF section should be included in the config
file. However, I get "....is not supported, or not recognized in this
context" for each of the following options:
fullSamples 100
hideJacobian no
outputFreq 100
applyBias yes
Also, is there a way to use "-DCOLVARS_DEBUG" if we choose the precompiled
namd version?
Some advice would is requested...
Thanks,
Neela
(ps: Sorry to have to bother you so much)
On Thu, Aug 20, 2009 at 3:46 AM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>wrote:
> Hi Neela, the example of input file for a simple "distance" variable
> in the new Users Guide can be taken almost literally.
>
> group1, group2, group3 and group4 are needed for a dihedral, but you
> can take as example group1 and group2 from the distance input above.
>
> Giacomo
>
> ---- ----
> Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science
> Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> work phone: (+1)-215-204-4216
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_<at>_gmail.com
> ---- ----
>
>
>
> On Wed, Aug 19, 2009 at 6:03 AM, Neelanjana Sengupta<senguptan_at_gmail.com>
> wrote:
> > Hi Giacomo and others,
> >
> > The CVS version of the user's guide containing colvars was more
> informative.
> > Based on it, this is how the component part of my colvars config file
> looks
> > like, for a single dihedral component:
> >
> > dihedral {
> > myatoms {
> > group1 { 1 }
> > group2 { 2 }
> > group3 { 3 }
> > group4 { 4 }
> > atomsFile component.pdb
> > atomsCol O
> > atomsColValue 4.00
> > psfSegID TRAN
> > }
> > }
> >
> > However, I am getting this error message at runtime:
> >
> > colvars: Initializing a new collective variable.
> > colvars: # name = omgprm
> > colvars: Initializing a new "dihedral" component.
> > colvars: # componentCoeff = 1 [default]
> > colvars: # componentExp = 1 [default]
> > colvars: # oneSiteSystemForce = off [default]
> > colvars: Error: definition for atom group "group1" not found.
> >
> > Can I please get some help and some pointers with this?
> >
> > Thanks a lot.
> > Regards,
> > Neela
> >
> >
> >
> >
> >
> > On Mon, Aug 17, 2009 at 7:16 PM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>
> > wrote:
> >>
> >> Hi Neela, I didn't feel necessary to repeat the instructions on how to
> >> download the CVS (i.e. development) version of NAMD, because the
> >> relevant webpage is linked directly from the NAMD main webpage ("Build
> >> from Source Code").
> >>
> >> I paste its address here again for your convenience.
> >>
> >> http://www.ks.uiuc.edu/Research/namd/development.html
> >>
> >> Giacomo
> >>
> >> ---- ----
> >> Giacomo Fiorin
> >> ICMS - Institute for Computational Molecular Science
> >> Temple University
> >> 1900 N 12 th Street, Philadelphia, PA 19122
> >> work phone: (+1)-215-204-4216
> >> mobile: (+1)-267-324-7676
> >> mail: giacomo.fiorin_<at>_gmail.com
> >> ---- ----
> >>
> >>
> >>
> >>
> >
> >
>
-- ~~~~~~~~~~~~~~~~~~~~ Neelanjana Sengupta, PhD Physical Chemistry Division National Chemical Laboratory Dr. Homi Bhaba Road Pune 411008, India Phone: +91-20-2590 2087 Fax: +91-20-2590 2636 ~~~~~~~~~~~~~~~~~~~~
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