Re: Colvars Configuration File

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Aug 19 2009 - 17:16:24 CDT

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
>> ---- ----
>>
>>
>>
>>
>
>

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