Re: Colvar with variable axis

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Mar 12 2015 - 08:53:45 CDT

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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