Re: colvars to restrain peptide close to lipid

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Apr 26 2017 - 15:31:33 CDT

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
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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