From: nicolas martin (nicolasmartin973_at_gmail.com)
Date: Thu Apr 10 2014 - 08:40:18 CDT
But isn't the spinangle computing the rotation of the center of geometry of
the group selected around the defined axis ? I understood that from what
I've read on colvar::spin_angle Class Reference page.
2014-04-10 15:34 GMT+02:00 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>:
> 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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