From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Thu Apr 27 2017 - 15:11:17 CDT
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? I am using NAMD 2.10
because the REST2 support is not available to the newer versions yet.
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
>
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