Re: Colvars Configuration File

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Mon Aug 17 2009 - 08:46:45 CDT

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
---- ----

On Mon, Aug 17, 2009 at 12:52 AM, Neelanjana
Sengupta<senguptan_at_gmail.com> wrote:
> Hi,
> I am sorry if I sound naive, but this link did not provide the
> ug_colvars.tex file:
> http://www.ks.uiuc.edu/Research/namd/cvs2html/namd2_ug__rf.html
>
> Can you please point out where I can download it from?
>
> Thanks,
> 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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