Re: colvars to restrain peptide close to lipid

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 27 2017 - 15:13:14 CDT

On Thu, Apr 27, 2017 at 4:11 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> Hi Giacomo,
>
> Thanks for the input. Did not know this before. Will the use of forceNoPBC
> increase the overhead when running NAMD on the HPC?
>

No.

> I am using NAMD 2.10 because the REST2 support is not available to the
> newer versions yet.
>

Yes, I remember... :-(

>
>
> Chitrak.
>
> On Wed, Apr 26, 2017 at 7:46 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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
>>
>
>

-- 
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

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