From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 10 2014 - 08:34:25 CDT
C4 in butane has three hydrogens, all free to rotate around the C3-C4 bond.
Giacomo
On Apr 10, 2014 9:30 AM, "nicolas martin" <nicolasmartin973_at_gmail.com>
wrote:
> Dear Giacomo, dear all,
>
> I'm sorry for the misent messages I got troubles to do that simple thing..
>
> You are right maybe I should have explained what was my point of making a
> comparison between both spinangle and dihedral which are too different
> things. I know how to manage the colvar dihedral and I find it pretty
> simple to use but I cannot say that about spinangle. I figure out that in
> special cases, if I understood right reading the UG, spinangle and dihedral
> might give the same result (maybe just with a shift due to the reference
> structure).
>
> To illustrate what I've just said :
>
> If C1, C2 and C3 remain fixed by for example using the keyword fixedAtoms
> or applying an absolute restrain on them, defining the axis of rotation in
> the colvar spinangle as C2-C3 bond. and using the C4 and its H to measure
> the spinangle, I thought that I could correlate dihedral and spinangle. But
> I was obviously mistaken.
>
> My final goal is to compute the PMF along a coordinate reaction e.i. the
> twisting angle between the trans-membrane and extracellular domain of a
> receptor. And doing so with and without a ligand. What do you think would
> be the best approach to do so ? I have been watching as well to the
> possibility of SMD. What is you opinion about applying it to my problem ?
>
> Thank you again for your help and reactivity, bests,
>
> NM
>
>
> 2014-04-09 18:18 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
>
>> Hello Nicolas, here are some suggestions:
>> - please send all your emails to the mailing list, not only part of them;
>> - butane is a tiny molecule, but still fairly flexible: please try a
>> really rigid one such as benzene or phenol instead of setting constraints;
>> - when you constrain/restrain the positions of heavy atoms, the two
>> terminal methyl groups can still rotate;
>> - a dihedral angle and a spinangle are two different quantities: your
>> setup is only for the latter, if you wish to define the dihedral
>> C1-C2-C3-C4, you should do so by using a "dihedral" function.
>>
>> Regards,
>> Giacomo
>>
>>
>>
>> On Wed, Apr 9, 2014 at 11:40 AM, nicolas martin <
>> nicolasmartin973_at_gmail.com> wrote:
>>
>>> Dear Giacomo,
>>>
>>> After reading your message I went back to my first idea which was
>>> developing my method on a way smaller molecule : butane. As you mentioned I
>>> tried to solve the problem of RMSD on both group by restraining them. I
>>> still have those Warnings and actually cannot align my reference group in
>>> VMD. In another hand, I can see clearly the spinangle colvar going from 0
>>> to 40 as asked but the dihedral angle itself is not moving... I think this
>>> might be due to a failure of the alignment.
>>>
>>> Here is the input file :
>>>
>>> colvar {
>>> name spinangle
>>> spinangle {
>>> axis (-1.408,-0.537,-0.317) # axis C2 C3
>>>
>>> atoms {
>>> atomNumbers 11 12 13 14 #..moving group
>>> centerReference on
>>> rotateReference on
>>> refPositionsGroup { #..reference group
>>> atomNumbers 1 5 8
>>>
>>> }
>>> refPositionsFile input/ref.pdb
>>> refPositionsCol O
>>> refPositionsColValue 1.00
>>> }
>>>
>>> refPositionsFile input/ref.pdb
>>>
>>> }
>>> }
>>> harmonic {
>>> name harmonic
>>> colvars spinangle
>>> forceConstant 0.0060923
>>> centers 0
>>> targetCenters 40
>>> targetNumSteps 1000
>>> targetNumStages 11
>>> }
>>> colvar {
>>> name rmsd
>>> rmsd {
>>> atoms { atomNumbers 11 12 13 14 }
>>> refPositionsFile input/ref.pdb
>>> }
>>> }
>>> harmonic {
>>> name rmsd_hamonic
>>> colvars rmsd
>>> forceConstant 100
>>> centers 0
>>> }
>>>
>>
>>
>
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