Re: Colvars Configuration File

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Sat Aug 15 2009 - 08:56:38 CDT

Hi Neela, "globalOption", "colvarOption", "componentOption"
"componentLongOption"... are just examples to illustrate the format.

"colvarOption" may be "name", for instance (the name of the colvar).

The documentation is perhaps clearer in the CVS version: grab the file
ug_colvars.tex and recompile the Users' Guide to have an actual
example.

Please also note that all the ABF options are in the colvars
configuration file, not the NAMD file.

Finally, you'll need colvarsInput only when you restart.

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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On Sat, Aug 15, 2009 at 3:16 AM, Neelanjana Sengupta<senguptan_at_gmail.com> wrote:
> Dear NAMD community,
>
> I intend to calculate the PMF of a small biomolecule as a function of just
> one of its dihedral angles (which I call omega_prime), using the Adaptive
> Biasing Force module in NAMD 2.7. This should be s starightforward 1-D
> calculation.
>
> For this purpose, I have added the following lines in my namd input file for
> an isobaric-isothermal simulation:
>
> ###### Collective Variables Section ####################
> colvars on
> colvarsConfig config_colvars1.inp
> colvarsInput config_colvars2.inp
>
> ###### ABF Section ####################
> fullSamples 100
> hideJacobian no
> outputFreq 100
> # Reading gradient and sampling files:
> #inputPrefix
> applyBias yes
> ######################################
>
>
> However, I am having a bit of trouble in putting together my colvars input
> file. I tried to follow the example and the instructions given in the
> manual, to put this together:
> #########################################
> globalOption ??
> colvar {
> name omgprm
> width 1.0
> # Assuming colvars treats dihedrals in degrees:
> lowerBoundary -10.0
> upperBoundary 175.0
> # lowerWallConstant 0.03 # Is it necessary to supply these?
> # upperWallConstant 0.08
> outputValue on
> outputVelocity off
> outputSystemForce off
> outputAppliedForce on
> extendedLagrangian off
> componentExp 1
> componentCoeff 1.0
>
> # Defining the components:
> colvarOption ??
> dihedral {
> componentOption ??
> componentLongOption {
> ??
> }
> }
>
> # atom group definitions:
> myatoms {
> psfSegID TRAN
> atomsFile component.pdb
> atomsCol O
> atomsColValue 4.00
> }
> }
>
> biastype1 {
> name ??
> colvars omgprm
> }
> #########################################
>
> I did not quite understand from the manual what the "globalOption",
> "colvarOption", "componentOption" and the "componentLongOption" stand for.
> The form of the variable "mybias" is also not clear to me.
>
> Some help with this would be greatly appreciated.
>
> Thanks and regards,
> Neelanjana Sengupta
>
> --
>
>

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