Re: Umbrella sampling with hbond

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Mar 24 2012 - 12:52:17 CDT

Hello Christy, you need to specify atom numbers for hBond as in "acceptor
5658" and "donor 2035".

http://www.ks.uiuc.edu/Research/namd/2.9b1/ug/node55.html#SECTION0001322140000000000000

On Thu, Mar 22, 2012 at 8:05 PM, Payne, Christy <Christy.Payne_at_nrel.gov>wrote:

> I am attempting to setup a set of umbrella sampling simulations using the
> hbond colvar; however, I get an error with the acceptor selection in my
> colvar configuration file ( Error: in parsing "acceptor"). I have copied
> my colvar configuration file below. There doesn't appear to be a problem
> with the donor selection, as I have moved it before the acceptor selection
> without issue. I would greatly appreciate any suggestions as to what I may
> be doing incorrectly here.
>
> Thanks in advance!
> Christy
>
>
> colvarsTrajFrequency 100
> analysis on
>
>
> colvar {
> name catres
>
> # Estimate of the typical fluctuation amplitude for this collective
> variable
> width 0.01
>
> # RC values between 0 and 1
> lowerboundary 0
> upperboundary 1
>
> # Values at which to start applying biasing potential
> lowerWall 0.01
> upperWall 0.99
>
> # Bias potential force constants
> lowerWallConstant 2.5
> upperWallConstant 2.5
>
> # Output the applied force in the .traj file
> outputAppliedForce on
>
> # Reaction coordinate (or collective variable to be used)
> # Here it is hbond which goes from an nondimensional value of 0 to 1
>
> hbond {
>
> # Acceptor is glycosidic oxygen
> acceptor {
> atomNumbers 5658
> }
>
> # Donor is OD2 of D221
> donor {
> atomNumbers 2035
> }
>
>
> # These are the default values for hbond
> cutoff 3.3
> expNumer 6
> expDenom 8
> }
> }
>
> # Application of harmonic potential
> harmonic {
> name umbsamp
> colvars catres
> centers 0.5
> forceConstant 2.5
> }
>
> histogram {
> colvars catres
> outputFreq 100
> }
>
>

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