Re: colvars to restrain peptide close to lipid

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun May 21 2017 - 11:31:42 CDT

At distances smaller than half a box length, the values with "forceNoPBC
on" will be identical to those without the flag. If you have kept the same
setup as posted earlier, this could simply be a sampling issue?

Giacomo

On Sat, May 20, 2017 at 5:10 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> 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
>>
>
>

-- 
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 : Sun Dec 31 2017 - 23:21:18 CST