Re: need help in using colvars option

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Aug 27 2012 - 17:54:09 CDT

Hello Sudipta:

1) Any keyword that you don't know the meaning of, don't include it: leave
the default values for that.
2) It would help others to help you if you reported the exact numbers, when
you say that the values reported by NAMD and VMD are "significantly
different".
3) If you want to restrain the distance variable around one value, use the
value with PBC.
4) Decide whether you want to restrain around one value, or within an
interval (you actually wrote the latter).
5) Increase the force constants until you are satisfied, or the simulation
blows up in pieces.

Giacomo

On Mon, Aug 27, 2012 at 6:41 PM, sudipta <sudipta.mml_at_gmail.com> wrote:

> Hi All,
>
> I need to perform a restrained simulation of protein molecule. In this
> regard, I need your help. To perform that simulation, I have chosen two
> groups of protein atoms and COM distance between these two groups of atoms
> is the collective variable. The input parameters are given below,
>
> colvarsTrajFrequency 100
> colvarsRestartFrequency 100
>
> colvar {
> name comdis
>
> width 5.0
>
> lowerboundary 0
> upperboundary 133.0
>
> lowerWallConstant 0.1
> upperWallConstant 0.2
>
> outputAppliedForce on
> outputVelocity on
> outputSystemForce on
>
> distance {
>
> group1 {
> atomnumbers {3442 4835}
> }
> group2 {
> atomnumbers {4137 4140}
> }
> }
> }
>
> I have manually calculated the COM distance between these two group of
> atoms and the value is significantly differ with the namd output which is
> written in .colvars.traj file. The two values are 132.33 (35.3 with PBC) A
> and ~60 A. My aim is to sample the protein molecule in such a manner where
> the distance between those two defined group of atoms of the protein
> molecule fluctuate around 132.33 A with some standard deviation (say 5 A).
> So how to reach my aim. Any suggestion will be highly appreciated.
>
> Thanks in advance
> Sudipta
>

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