Re: colvars to restrain peptide close to lipid

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Apr 26 2017 - 15:15:10 CDT

Just realized there is a typo in what I posted. I am using "distanceZ", not
"distance Z" (no space between distance and Z) in my simulation.

On Wed, Apr 26, 2017 at 4:01 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> Hi NAMD users,
>
> I am simulating a peptide-lipid system where the peptide is placed on the
> top of the lipid. To keep the peptide from interacting with the bilayer of
> the periodic image, I used the upperWallConstant colvars feature, defined
> on the "distanceZ" between a peptide atom and a lipid atom. Here is the
> script I used
>
> colvar {
> distance Z {
> ref {
> # This file has the "beta" column of the
> lipid atom set to 1, everything else set to 0
> atomsFile lipidBeta.pdb
> atomsCol B
> atomsColValue 1.0
> }
> main {
> # This file has the "beta" column of
> the peptide atom set to 1, everything else set to 0
> atomsFile peptideBeta.pdb
> atomsCol B
> atomsColValue 1.0
> }
> }
>
> upperBoundary 70.0
> upperWallConstant 1000.0
> }
>
>
>
> However, in the simulation, I do find the colvars distance transiently
> crossing the upper boundary (which is ok for my simulation), and then
> eventually the peptide starts interacting with the lipid in the periodic
> image.
>
> Does anyone know if I implemented the colvars correctly?
>
> Also, I had "wrapAll on" which meant once the peptide started interacting
> with the periodic image, it came to the bottom of the peptide and now the
> colvars distance had a negative value, which obviously was still "within"
> the upper bound. Should I also use a lowerWallConstant to take care of this?
>
>
> Thanks for the help,
> Chitrak.
>

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