From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed May 18 2011 - 09:40:25 CDT
Dear Maiti,
At first glance, your input looks correct. For this simulation, you
don't even need the options width, lower/upperBoundary, or
lower/upperWallConstant.
What matters for umbrella sampling is the target value (centers) and
the force constant, both defined in the harmonic bias. Then it is up
to you to choose the protocol that you want to use to run the
different windows for your umbrella sampling calculation. Once you
know that, the harmonic bias has moving restraint options that could
help you implement what you have in mind.
Best,
Jerome
On 18 May 2011 04:52, Buddhadev Maiti <chebm_at_langate.gsu.edu> wrote:
> Dear NAMD Users,
> I am trying to prepare input files for umbrella sampling using NAMD-2.7 with colvar option. But I am not getting clear information in NAMD-2.7 manual. Could you please help me about Distance.in file. I am pasting below. Regarding centers, which value do I need to choose. The initial distance between the two groups is 5.77 Angstrom. Is it necessary to keep width, lowerwallconstant and upperwallconstant.
> Have a nice day,
> Thanks,
> Maiti
>
> Distance.in:
>
> Colvarstrajfrequency 1000
> Colvarsrestartfrequency 1000
> colvar {
> name ProjectionZ
> lowerboundary 5.52
> upperboundary 6.02
> distanceZ {
> main {
> atomnumbers { 6633 6640 6654 6661 6675 6694 6716 6735 }
> }
> ref {
> atomnumbers { 1681 1703 1719 1730 1742 1763 1778 1795 }
> }
> axis (-0.50, -0.56, -0.64 )
> }
> }
> harmonic {
> colvars ProjectionZ
> centers 5.77
> forceConstant 10.0
> }
>
>
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