From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Apr 26 2017 - 17:22:37 CDT
Oops, forgot to reply to the group.
---------- Forwarded message ----------
From: Chitrak Gupta <chgupta_at_mix.wvu.edu>
Date: Wed, Apr 26, 2017 at 6:22 PM
Subject: Re: namd-l: colvars to restrain peptide close to lipid
To: Jeff Comer <jeffcomer_at_gmail.com>
Hi Jeff,
Thanks for the help. Yes, indeed, my box dimensions are 128A in the
Z-dimension.
However, I was expecting that the restraint would be on the distanceZ that
I defined. The colvar is defined as the distance between the "main" and the
"ref", so shouldn't that be independent of the box dimension? Or am I
missing something here?
Chitrak.
On Wed, Apr 26, 2017 at 4:31 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> Dear Chitrak,
>
> Here's a possible explanation. What is the size of your system along
> z? Have a look at the .colvars.traj file. Do you see discontinuous
> jumps? If your system is smaller than 140.0 Å along the z axis then
> your colvar will never reach 70. For example, if the system has a size
> along z of 100 Å, then the colvar will hop from +50 to –50 and never
> approach 70. If this is the case, you probably need to set your
> upperBoundary to something smaller, for instance upperBoundary=48.
>
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311 <(785)%20532-6311>
> Website: http://jeffcomer.us
>
>
> On Wed, Apr 26, 2017 at 3:15 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
> wrote:
> > 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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