From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 10 2014 - 08:56:01 CDT
Yes but the axis goes through the group's center of geometry.
On Apr 10, 2014 9:40 AM, "nicolas martin" <nicolasmartin973_at_gmail.com>
wrote:
> 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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