Re: How to remove center of mass translation of macromolecule

From: Teerapong Pirojsirikul (tpirojsi_at_ucsd.edu)
Date: Thu Jun 13 2013 - 20:56:29 CDT

That answered the question why only values in z axis are the same
(neglecting the sign because it depends on the order of group1 and group2
defined). The position in x and y dimension of the ion are beyond half the
box length. So in this case the different coordinate outputs from colvar
and dcd file are unavoidable if I want to measure the distance between the
ion and dummy atom at (0, 0, 0), right?

Best,
Tee

2013/6/13 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>

> Not only start with your group of atoms close to the dummy atom, but make
> sure that the two groups never go farther away than half the box length.
>
> Giacomo
>
>
> On Thu, Jun 13, 2013 at 8:40 PM, Teerapong Pirojsirikul <tpirojsi_at_ucsd.edu
> > wrote:
>
>> Hello Giacomo,
>>
>> My unit cell parameters are (extracted from my log file)
>>
>> Info: PERIODIC CELL BASIS 1 68.078 0 0
>> Info: PERIODIC CELL BASIS 2 0 60.0632 0
>> Info: PERIODIC CELL BASIS 3 0 0 78.8933
>> Info: PERIODIC CELL CENTER 36.8 32.6 42.56
>>
>> Probably this is the case as you mentioned? What if I want the colvar
>> outputs the same result as extracted from dcd file, what should I do then?
>> Start with the system where PBC center at 0, 0, 0??
>>
>> Best,
>> Tee
>>
>>
>> 2013/6/13 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>>
>>> Hello Tee, what are your unit cell parameters? It may be possible that
>>> the closest periodic image to the origin is not (37.129, 36.890,
>>> 33.701) but the values you see in the output...
>>>
>>> Giacomo
>>>
>>>
>>> On Thu, Jun 13, 2013 at 6:38 PM, Teerapong Pirojsirikul <
>>> tpirojsi_at_ucsd.edu> wrote:
>>>
>>>> Hi Jerome,
>>>>
>>>> Thank you very much for your advice. I have tried both approaches out.
>>>> For the first suggestion, I have plotted the rmsd of the COM of the RNA
>>>> backbone and the values were running around 0.1. Together with rotation
>>>> blocking, I could remove both translation and rotation of the RNA.
>>>>
>>>> As for the second approach, as I understand, the MD simulation is
>>>> performed regularly, which is there might be rotation and translation of
>>>> the RNA, but the colvar output will return the distance vector between the
>>>> ion and, in the case of your input file, dummy atom at position (0,0,0) in
>>>> the frame of reference defined in group1, isn't it?
>>>>
>>>> I first tried out with this input colvar file,
>>>>
>>>> colvar {
>>>> name ionPosition
>>>> distanceVec {
>>>> group1 {
>>>> atomNumbers 2020
>>>> }
>>>> group2 {
>>>> dummyAtom (0.0, 0.0, 0.0)
>>>> }
>>>> }
>>>> }
>>>>
>>>> The initial position of Mg from PDB file used to start the simulation
>>>> is (37.129, 36.890, 33.701) But the first few lines from colvar traj I got
>>>> are
>>>> # step ionPosition
>>>>
>>>> 0 ( 3.09493954130363e+01 , 2.31730595523354e+01 ,
>>>> -3.37012114861363e+01 )
>>>> 1000 ( 3.11665756227577e+01 , 2.32411814446486e+01 ,
>>>> -3.36415457741733e+01 )
>>>> 2000 ( 3.09509987444541e+01 , 2.28119750757673e+01 ,
>>>> -3.34979393701572e+01 )
>>>> ...
>>>>
>>>> What is wondering me is why at the step 0, the distance vector returned
>>>> different values from the initial position in PDB file. I also extracted
>>>> the Mg postions at other time steps from the dcd file and they didn't seem
>>>> to be in agreement with the colvar trajectory output as well. If the
>>>> coordinates in a pdb file typically refer to the origin at (0, 0, 0), I
>>>> think both outputs should result the same thing.
>>>>
>>>> Please correct me if I'm wrong.
>>>>
>>>> Best,
>>>> Tee
>>>>
>>>>
>>>> 2013/6/12 Jrme Hnin <jerome.henin_at_ibpc.fr>
>>>>
>>>>> Hi Tee,
>>>>>
>>>>> The simplest way to restrain the translations of the RNA molecule is
>>>>> to restrain a distance coordinate linking its center of mass to a dummy
>>>>> atom (that is, a fixed point). The input for that restraint would be:
>>>>>
>>>>> colvar {
>>>>> name RNAcenterDistance
>>>>>
>>>>> distance {
>>>>> group1 {
>>>>> atomNumbers 1 2 3 4 5 # RNA reference atoms
>>>>> }
>>>>> group2 {
>>>>> dummyAtom (42.0, 42.0, -42.0) # set to initial position of
>>>>> group1 center
>>>>> }
>>>>> }
>>>>> }
>>>>>
>>>>> harmonic {
>>>>> colvars RNAcenterDistance
>>>>>
>>>>> centers 0.0
>>>>> forceConstant 10.0
>>>>> }
>>>>>
>>>>>
>>>>> Note that if you use the colvars module, you might also be able to do
>>>>> your calculation without restraining the RNA molecule at all, neither its
>>>>> translation nor its rotation. You can do that by measuring the coordinate
>>>>> of interest (here the 3D position of the ion as a distanceVec coordinate)
>>>>> in a frame of reference linked to the RNA, that is, rotated and translated
>>>>> to match global motion of the RNA molecule. The complete input would then
>>>>> look like this:
>>>>>
>>>>>
>>>>> colvar {
>>>>> name ionPosition
>>>>>
>>>>> distanceVec {
>>>>>
>>>>> group1 {
>>>>> atomNumbers 4242 # ion
>>>>>
>>>>> centerReference # use relative coordinates
>>>>> rotateReference # (translated and rotated frame of
>>>>> reference)
>>>>> refPositionsGroup { # work in frame of reference based on
>>>>> RNA molecule
>>>>> atomsFile ref.pdb # from separate file
>>>>> atomsCol B # RNA reference atoms tagged in column
>>>>> B
>>>>> }
>>>>> refPositionsFile ref.pdb # initial coordinates for reference
>>>>> group
>>>>> }
>>>>>
>>>>> group2 {
>>>>> dummyAtom (0.0, 0.0, 0.0) # arbitrary reference point for the
>>>>> ion position
>>>>> }
>>>>> }
>>>>> }
>>>>>
>>>>> The second group could also be a group of atoms within the RNA
>>>>> molecule, defining the active site - in that case, group2 should be
>>>>> calculated in the same local reference frame (re-using the options
>>>>> centerReference, refPositionsGroup, etc.)
>>>>>
>>>>> Cheers,
>>>>> Jerome
>>>>>
>>>>>
>>>>> ----- Original Message -----
>>>>> >
>>>>> > Hi NAMD users,
>>>>> >
>>>>> >
>>>>> > I have been looking for how to remove center of mass translation of a
>>>>> > macromolecule. I have read many threads regarding this issue in the
>>>>> > mailing list but still got confused. I'm working on a sampling
>>>>> > problem and want to reconstruct a free energy surface as a function
>>>>> > of Cartesian coordinates (x,y, and z) of a certain ion moving in an
>>>>> > active site of an RNA molecule. As a result, I need to perform the
>>>>> > MD simulation at a fix orientation (by removing rotation and
>>>>> > translation of the RNA). I can successfully fix the rotation by
>>>>> > blocking the backbone of the molecule using orientation colvar
>>>>> > module. But I'm wondering what is the easiest way to remove the
>>>>> > translation of the RNA. I have tried fixing one atom but am curious
>>>>> > whether this will cause any artificial dynamics to my system or to
>>>>> > the fixed atom. Also I have seen many people talking about dummy
>>>>> > atom but don't quite have a clear idea how to make use of it. Any
>>>>> > advice would be appreciated.
>>>>> >
>>>>> >
>>>>> > Tee
>>>>>
>>>>
>>>>
>>>
>>
>

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