Re: FixedAtoms and Reference group in spinangle colvar

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun May 11 2014 - 17:27:29 CDT

Hello Nicolas, as I mentioned earlier and Jérôme pointed out as well,
butane is a very small and flexible molecule, not suitable for defining a
rigid-body rotation. Including the hydrogens won't help, because they are
even more flexible than the carbon atoms, in particular the methyl
hydrogens which can rotate freely around the C1-C2 bond. (I wrote to you
about this too).

In short, NAMD can simulate butane just fine, but your assumption that you
can have a large enough rigid section (more than 3 atoms) is incorrect.

Please, do try with a molecule that includes a rigid group like a benzyl
ring. (See my previous email).

Thank you
Giacomo

On Sun, May 11, 2014 at 5:52 PM, nicolas martin
<nicolasmartin973_at_gmail.com>wrote:

> Hi Jérôme,
>
> Thank you for your answer. I tried to include in my refgroup selection the
> hydrogens around C1 and C2. So the selection contains now 8 atoms. But
> still, the result remains the same.
>
> Do you think skipping this step assuming that it is due to the fact that
> butane is not really what NAMD is made to work with and going to the next
> step which is actual work on my protein would be a good idea? I mean how
> can I make sure that I am not mistaken there and that it’s just a matter of
> size and not because of me not fully understanding how to use that
> powerful tool ?
>
> Thank you again, bests,
>
> NM
>
>
> 2014-05-09 20:53 GMT+02:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>
> Hi Nicolas,
>>
>> I think the most likely issue is that 3 atoms is not sufficient for the
>> refPositionsGroup to be fitted properly. With this setup you should be able
>> to make it a little larger.
>>
>> Cheers,
>> J
>>
>> ----- Original Message -----
>> > Dear NAMD users,
>> >
>> > I ask for your help once more concerning my issues with spinangle.
>> > I'm working on butane (I know this is not ideal due to the fact that
>> it's a
>> > small molecule that could create problems for fittings) and I'm trying
>> to
>> > use spinangle covlar to compute a PMF along the rotation of the dihedral
>> > angle defined by C1 C2 C3 and C4. This is done on purpose because I
>> plan to
>> > move on a protein so the obviously solution of using a dihedral colvar
>> > isn't my first choice. C1 C2 and C3 are included into the reference
>> group
>> > and if I'm right this allows me to cancel any rotation or translation
>> > effects to THEN compute the spinangle with contains as well a fitting
>> > between a reference structure a the current one (superimposed with the
>> > atoms specified in refgroup as said before).
>> >
>> > I tried first the following colvar defnition and in addition used the
>> > keyword fixedAtoms to fix C1 C2 and C3 and I got a nice match between
>> this
>> > PMF and the one obtained with a simple dihedral colvar (my reference).
>> >
>> > Then I removed the fixedAtoms keyword and here is my problem, my PMF is
>> not
>> > anymore what I expected.
>> >
>> > So please tell me where is my mistake? I thought it would be the same
>> and I
>> > wouldn't need to fix any atoms since I'm fitting C1 C2 and C3 to the
>> > reference structure...?
>> >
>> > And if I move on my protein, how can I then make sure than the diffusion
>> > (even if it shoul be really less than butane's diffusion) isn't
>> introducing
>> > a bias in my PMF?
>> >
>> >
>> > Thanks a lot in advance for your help ,
>> >
>> > NM
>> >
>> >
>> > spinangle.in :
>> >
>> > colvarsTrajFrequency 1
>> >
>> > colvar {
>> > name spinangle
>> > spinangle {
>> > axis (-1.408,-0.537,-0.317) # axis of bond C2 C3
>> >
>> > atoms {
>> > atomNumbers 8 9 10 11 #..moving group
>> > centerReference on
>> > rotateReference on
>> > refPositionsGroup { #..reference group
>> > atomNumbers 1 5 8
>> > }
>> > refPositionsFile ../input/buta.pdb
>> > }
>> > refPositionsFile ../input/buta.pdb
>> > }
>> > }
>> >
>> >
>> >
>> > harmonic {
>> > name harmonic
>> > colvars spinangle
>> > forceConstant 0.006
>> > centers XXXX
>> > }
>> >
>>
>
>

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