From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Mar 12 2015 - 08:25:54 CDT
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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