Re: ABF Colvars Configuration File

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Thu Aug 20 2009 - 10:59:35 CDT

Hi Neela, those are ABF keywords, so when I wrote to include in the
colvars config file, I didn't mean at the top level, but in the abf
block.

Regards,
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 Thu, Aug 20, 2009 at 10:21 AM, Neelanjana
Sengupta<senguptan_at_gmail.com> wrote:
> 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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