From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Sat May 20 2017 - 16:10:35 CDT
Hi Giacomo and Jeff,
This is a rather late update, but here is something I noticed. Initially
(when applying the restraint without forceNoPBC) I was observing my peptide
detach from the bilayer which was in fact expected. Now that I am using
forceNoPBC, the peptide no longer detaches. While this isn't entirely
impossible, I am wondering whether this force constant might have an effect
on preventing the detachment. Any inputs?
On Thu, Apr 27, 2017 at 4:13 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
>
>
> 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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