Re: How to remove center of mass translation of macromolecule

From: Teerapong Pirojsirikul (tpirojsi_at_ucsd.edu)
Date: Thu Jun 13 2013 - 19:40:23 CDT

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 Jérôme Hénin <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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