Re: Colvar with variable axis

From: Mitchell Gleed (aliigleed16_at_gmail.com)
Date: Thu Mar 12 2015 - 10:49:21 CDT

Thank you both so much for your help with this--what an excellent feature!
I will give it a shot and see how it goes.

On Thu, Mar 12, 2015 at 7:53 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi Mitchell,
>
> The refPositionsGroup is internal to the atom group, and entirely
> transparent to the colvar component such as tilt. Essentially, the atom
> group will report rotated/translated coordinates which will be used to
> calculate the tilt.
>
> Right now your input would restrain the ligand at a height of 1 Angstrom
> along the z axis (within the frame of reference of the protein if it moves
> from its initial position).
>
> Jerome
>
> On 12 March 2015 at 14:25, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> The place seems OK.
>>
>> refPositionsGroup or any of the roto-translational options don't really
>> apply to a dummyAtom group: because it is not made by real atoms, it can
>> move or rotate over time.
>>
>> On Thu, Mar 12, 2015 at 1:59 PM, Mitchell Gleed <aliigleed16_at_gmail.com>
>> wrote:
>>
>>> Thank you for pointing out ref2, not sure how I missed it. So, if I
>>> understand correctly, the axis is dynamically calculated as the vector
>>> formed between ref and ref2, right? (analogous to COOR AXIS in CHARMM).
>>> Seems straightforward enough.
>>>
>>> The refPositionsGroup implementation is a little less clear to me but I
>>> think may be the better option, if I understand it properly: defining a
>>> refPositionsGroup would rotate/translate the collective variable with
>>> respect to a reference group of atoms; so in this case, I would use
>>> coordinates of interest (e.g. protein BB atoms) and the colvar output would
>>> be corrected relative to the reference, as if the channel axis were the Z
>>> axis.
>>>
>>> I'm not sure if I've put the refPositionsGroup, etc. in the right place
>>> or whether dummyAtom or axis still have the same meaning. Here's an attempt
>>> at a configuration for the colvar including refPositionsGroup, in which I
>>> hope to restrain the center of mass of a ligand to a dummy atom 1 Ang away
>>> from the principal axis, let me know if I'm on the right track:
>>>
>>> ----------
>>>
>>> colvar {
>>> name ligand
>>> distanceZ {
>>> ref {
>>> dummyAtom (0.0, 0.0, 1.0)
>>> }
>>> main {
>>> atomsFile system_ligand.pdb
>>> atomsCol B
>>> atomsColValue 1.00
>>> centerReference
>>> rotateReference
>>> refPositionsGroup {
>>> atomsFile system_proteinbb.pdb
>>> atomsCol B
>>> atomsColValue 1.00
>>> }
>>> refPositionsFile system_proteinbb.pdb
>>> }
>>> axis (0.0, 0.0, 1.0)
>>> }
>>> }
>>> harmonic {
>>> name restrligand
>>> colvars ligand
>>> centers 0
>>> forceConstant 1
>>> }
>>>
>>> ----------
>>>
>>> I would hope to implement a similar correction for tilt. I've used this
>>> colvar to restrain the tilt of a ligand relative to its reference
>>> coordinates (aligned to the system Z axis), and I'm curious if
>>> refPositionsGroup would work for that colvar, too, making the collective
>>> variable data relative to the channel axis rather than the system Z axis.
>>>
>>> Thanks for your help.
>>>
>>> On Thu, Mar 12, 2015 at 5:23 AM, Giacomo Fiorin <
>>> giacomo.fiorin_at_gmail.com> wrote:
>>>
>>>> Please check the documentation of distanceZ, and ref2 in particular.
>>>> If that doesn't work for you, please check refPositionsGroup as well.
>>>>
>>>> On Thu, Mar 12, 2015 at 12:01 PM, Mitchell Gleed <aliigleed16_at_gmail.com
>>>> > wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I've typically used the system Z axis (0,0,1) to represent a
>>>>> membrane-bound protein channel axis and to use it for collective variables
>>>>> such as distanceZ, spinAngle, etc.; but the channel axis is usually only
>>>>> approximated by the system Z axis, as the tilt of the protein with respect
>>>>> to Z varies somewhat during the course of a simulation. Is it possible to
>>>>> implement a collective variable such as distanceZ with an axis that
>>>>> continuously updates using the colvars module? I'm thinking maybe some of
>>>>> the other distance colvars (distanceVec, etc.) may hold the key, but I'm
>>>>> not quite sure if that's whats needed here.
>>>>>
>>>>> Mitch
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Giacomo Fiorin
>>>> Assistant Professor of Research
>>>> Institute for Computational Molecular Science (ICMS)
>>>> College of Science and Technology, Temple University
>>>> 1925 North 12th Street (035-07), Room 704D
>>>> Philadelphia, PA 19122-1801
>>>> Phone: +1-215-204-4213
>>>> https://icms.cst.temple.edu/members.html
>>>> http://giacomofiorin.github.io/
>>>>
>>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Assistant Professor of Research
>> Institute for Computational Molecular Science (ICMS)
>> College of Science and Technology, Temple University
>> 1925 North 12th Street (035-07), Room 704D
>> Philadelphia, PA 19122-1801
>> Phone: +1-215-204-4213
>> https://icms.cst.temple.edu/members.html
>> http://giacomofiorin.github.io/
>>
>>
>

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