From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Feb 05 2014 - 11:27:27 CST
I think that is mostly correct.
You don't need the "atomsFile" "atomsCol" or "atomsColValue". As long as
the numbers you've entered correspond to the serial atom number for the
input for your simulation. You can check by asking for "serial 8 7 15 13"
in VMD and make sure those atoms are the ones you want.
The only thing in the NAMD config file related to the restraints should be
what you have there, so that is all correct.
Yes, the force constant will be in the appropriate dimension for the colvar
being used. The center is just a single number here, and in the case of
all angles, it's assumed to be in degrees not radians.
On Wed, Feb 5, 2014 at 12:07 PM, Aaron Larsen <
alarsen_at_molbio.mgh.harvard.edu> wrote:
> Hello,
>
> I am attempting to perform umbrella sampling with a harmonic restraint on
> a dihedral angle of a nucleoside. Minimization sand unrestrained
> simulations are working well but I am having some difficulty proceeding
> onto umbrella sampling. I have read through the manual but there is not a
> lot of information regarding this process using dihedral angles in
> particular.
>
> The dihedral angle that I am attempting to restrain is O4'-C1'-N1-C2,
> otherwise known as the chi angle. This is the angle which describes the
> relative twist between the nuceobase and the sugar. I have prepared a
> modified version of my NAMD config file use for the simulation to include a
> term for colvars.
>
> The corresponding terms that I have placed in my config file are:
>
> #
> colvars on
> colvarsConfig
> U_wb_req_colversconfig.namd
> #
>
> In the colvars config file that I have pointed to, I have attempted to
> define the colvar corresponding to my dihedral angle with the atom numbers
> that correspond to the correct atoms in the appropriate pdb file. This is
> the contents of the colvarconfig file are:
>
> #Colversconfig file for diheral angles
> #
> colvarsTrajFrequency 100 # output
> values every 100 steps
> colvarsTrajAppend off
> analysis off
> #
> colvar {
> name chicolvar # chose a name to identify the variable
> outputSystemForce yes
> dihedral {
> group1 {
> atomNumbers 8
> }
> group2 {
> atomNumbers 7
> }
> group3 {
> atomNumbers 15
> }
> group4 {
> atomNumbers 13
> }
> }
> }
> atomsFile ../common/U_wb.pdb
> atomsCol O
> atomsColValue 2.0
> #
> harmonic {
> name chiharmonic #the name of your potential
> colvars chicolvar
> centers 0.0
> forceConstant 10.0
> }
>
> My questions are as follows:
>
> 1) Is it correct that the harmonic block be in the colversconfig file
> and not in the NAMD config file? Is there any additional information that
> should be in the NAMD config file other than simply the colvars block?
>
> 2) Is it correct that the value of 'centers' should be a single
> decimal corresponding to the desired dihedral angle that I would like
> center the constraint on?
>
> 3) Is it correct to assume that the force constant will be in units
> appropriate to a dihedral angle? In this case kcal·mol-1·deg-2?
>
> 4) When attempting to run the simulation, I am getting an error
> indicating that the term 'atomsFile' is not recognized by NAMD. Is this
> term no longer in use?
>
>
>
> Thank you very much for any input that you have.
>
>
> Best,
> Aaron
>
>
>
> --
> Aaron Larsen, Ph.D.
> Harvard University Department of Chemistry and Chemical Biology
> Harvard Medical School Department of Genetics
> E-mail: alarsen_at_molbio.mgh.harvard.edu
> Mobile: 617-319-3782
> FAX: 617-643-3328
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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