Re: using colvars to constrain two atoms in a direction

From: Hamed Fadaei (hamed.fadaei111_at_gmail.com)
Date: Wed Dec 14 2016 - 11:02:37 CST

-I tried the same script I had this time I added 4 or 5 atoms to the tilt
colvar but still I get the same error.

- Do you mean using two different distanceZ for two atoms so that I could
keep their orientation fixed? but in this case molecule won't be able to
move in Z direction. I want it to be free to move in any direction (Let's
just forget about umbrella sampling for a moment)

- Finally I just repeat my last question, is it possible to define an RMSD
constrain which just applies forces toward the best orientation of the two
atoms and not their position? Should I just give it a reference pdb file
with the two atoms at a desired ORIENTATION? Do you know of any good
example script for a similar thing?

Thanks,
Arman

On Wed, Dec 14, 2016 at 10:40 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Sorry, I overlooked the fact that you're using two atoms only... You
> can't do an orientational fit with less than 4 atoms. Try measuring their
> RMSD in VMD to see it.
>
> With two atoms, just use distanceZ to define their distance along the z
> axis. If they're bonded, the bond length won't change and distanceZ will
> be effectively the tilt.
>
> More about the molecule size: with two atoms, even if those are just two
> heavy atoms (e.g. methanol) you shouldn't need to restrain the orientation,
> the molecule is small enough to rotate while crossing the membrane.
>
>
> On Wed, Dec 14, 2016 at 11:34 AM, Hamed Fadaei <hamed.fadaei111_at_gmail.com>
> wrote:
>
>> Thank you very much Giacomo for your prompt response.
>> Actually since this happens at the very first step, there is no
>> trajectory to check.
>>
>> So, is it possible to define an RMSD constrain which just applies forces
>> toward the best orientation of the two atoms and not their position? Should
>> I just give it a reference pdb file with the two atoms at a desired
>> ORIENTATION?
>> Do you know of any good example script for a similar thing?
>>
>> Best,
>> Hamed
>>
>> On Wed, Dec 14, 2016 at 10:22 AM, Giacomo Fiorin <
>> giacomo.fiorin_at_gmail.com> wrote:
>>
>>> Hi Hamed, the error message indicates that the rotational fit (necessary
>>> to calculate the tilt variable) does not converge because the structure of
>>> the drug is not rigid. Please check the trajectory with VMD to see if this
>>> is the case.
>>>
>>> You could perhaps obviate this by replacing the tilt constraint with a
>>> RMSD constraint where only the translational fit is performed
>>> (centerReference on) but not the rotational (rotateReference off) is done
>>> to compute the RMSD.
>>>
>>> Giacomo
>>>
>>>
>>>
>>> On Wed, Dec 14, 2016 at 11:15 AM, Hamed Fadaei <
>>> hamed.fadaei111_at_gmail.com> wrote:
>>>
>>>> Dear NAMD usrs,
>>>>
>>>> I am trying to simulate a a drug translocationg from a membrane. The
>>>> drug is much longer in one direction and its orintation can be defined by a
>>>> single vector connecting two atoms (atom numbers 20 and 28 in my system).
>>>>
>>>> Now I need to constrain this vector with respect to the Z axis at
>>>> different angles by applying forces to these two atoms. I don't want to add
>>>> any extra constraints to the position of the atoms and drug can be free to
>>>> move as long as it keeps its angle with Z axis fixed.
>>>>
>>>> I tried to use "tilt" colvar by giving two ref points to define Z axis
>>>> and then constraining that tilt colvar to a harmonic :
>>>>
>>>> colvar {
>>>>
>>>> name tilt1
>>>>
>>>> tilt {
>>>>
>>>> atoms {
>>>>
>>>> atomNumbers {
>>>>
>>>> 28 20
>>>>
>>>> }
>>>>
>>>> }
>>>>
>>>> refPositions (0,0,0) (0,0,1)
>>>>
>>>> }
>>>>
>>>> }
>>>>
>>>> harmonic {
>>>>
>>>> colvars tilt1
>>>>
>>>> centers -0.9
>>>>
>>>> forceConstant 0.0
>>>>
>>>> }
>>>>
>>>> But when I run it, the system kinetic energy and temperature come out
>>>> as "nan" at step zero and I get the following error at the step one:
>>>>
>>>> colvars: Too many iterations in routine jacobi.
>>>>
>>>> FATAL ERROR: Error in the collective variables module: exiting.
>>>>
>>>>
>>>> Unfortunately I couldn't find anything related to that so I would be so
>>>> glad if you can help me. Besides, is this the best way to use tilt colvar
>>>> for my purpose or there might be a better way?
>>>>
>>>>
>>>> Best,
>>>>
>>>> Hamed
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Giacomo Fiorin
>>> Associate 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 <(215)%20204-4213>
>>>
>>> Scholar: http://goo.gl/Q3TBQU
>>> Personal: http://giacomofiorin.github.io/
>>> Lab page: https://icms.cst.temple.edu/members.html
>>>
>>> *"As computer programmers we have a responsibility to make sure that we
>>> run the computers instead of the computers running us."* - Steve
>>> Oualline
>>>
>>>
>>>
>>
>
>
> --
> Giacomo Fiorin
> Associate 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 <(215)%20204-4213>
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> Lab page: https://icms.cst.temple.edu/members.html
>
> *"As computer programmers we have a responsibility to make sure that we
> run the computers instead of the computers running us."* - Steve Oualline
>
>
>

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