Re: Colvars Configuration File

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Sat Aug 15 2009 - 10:12:55 CDT

Hi Giacomo,

Thanks. Where do I get the ug_colvars.tex file??

-Neela

On Sat, Aug 15, 2009 at 7:26 PM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>wrote:

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