From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Dec 14 2016 - 10:40:57 CST
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 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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