From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Apr 26 2017 - 18:46:50 CDT
Hi Chitrak, the distance is calculated using the minimum-image convention,
unless you used the forceNoPBC flag.
On Wed, Apr 26, 2017 at 6:22 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
> 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.
>> >
>> >
>>
>
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:15 CST