Re: Re: spinAngle

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jan 19 2012 - 05:13:15 CST

Is it perhaps possible to define dummy atoms together with centerRefrenceand
rotateRefrence,so that relative movement of the group is no longer
problematic?

Best regards,
Ajasja

On Wed, Jan 18, 2012 at 23:34, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:

> Hi Maiti, do you mean the rotation of a group's center of geometry around
> a fixed axis that doesn't pass through it? If so, I think you can define a
> dihedral angle where three groups are actually dummy atoms, and only one is
> the group of your interest, which you will use as either the 1st or 4th
> point in the dihedral. But in general, because molecules move around in
> NAMD, you should better define all groups out of real atoms to have a
> consistent reference system.
>
> Giacomo
>
> On Wed, Jan 18, 2012 at 5:28 PM, Buddhadev Maiti <bmaiti_at_gsu.edu> wrote:
>
>> Dear Giacomo,
>>
>> Thank you very much for your great help. Now it is clear for me. I have
>> another question if I am not bothering you, if there is NAMD implementation
>> of covar varible for simple rotation around the pivot point without
>> fitting. Could you please give me reply, ti will be great help for me.
>>
>>
>> Have a nice day,
>> Thanks again,
>> Maiti
>> ------------------------------
>> *From:* Giacomo Fiorin [giacomo.fiorin_at_gmail.com]
>> *Sent:* Wednesday, January 18, 2012 2:41 PM
>>
>> *To:* Buddhadev Maiti
>> *Cc:* namd-l
>> *Subject:* Re: spinAngle
>>
>> OK, I see your problem now. You're using the syntax of distanceZ to
>> define the axis, via the groups "ref" and "ref2".
>>
>> spinAngle is defined differently, with an explicit "axis", such as (0, 0,
>> 1) for example, and a single group of atoms, called "atoms", and the
>> reference coordinates define the rotation. It works the same as
>> "orientation".
>>
>> colvar {
>> spinAngle {
>> axis (xx, yy, zz)
>> atoms {
>> ....
>> }
>> refPositionsFile ....
>> }
>> }
>>
>>
>> On Wed, Jan 18, 2012 at 2:34 PM, Buddhadev Maiti <bmaiti_at_gsu.edu> wrote:
>>
>>> Dear Giacomo,
>>>
>>> Sorry for unclear reply. Now I writting clear email. I am trying to
>>> prepare covarsconfig file in below. But above file is not correct, sorry
>>> for that. I sent you for understanding my problem.
>>>
>>> ---------------------------------------------------------------------------------
>>> Colvarstrajfrequency 100
>>> Colvarsrestartfrequency 100
>>> colvar {
>>> name us
>>> spinAngle {
>>> main {
>>> atomnumbers { 3639 3648 3649 3646 3644 3645 3642 3640 }
>>> }
>>> ref {
>>> atomnumbers { 3637 3636 3634 3650 3652 }
>>> }
>>> ref2 {
>>> atomnumbers { 3655 3656 3659 3663 3682 }
>>> }
>>> }
>>> }
>>> harmonic {
>>> colvars us
>>> centers 1.31044732921888e+01
>>> forceConstant 10.0
>>> }
>>>
>>>
>>> -------------------------------------------------------------------------------------------------
>>> main and ref atoms indicates the angles of group of atoms and ref2
>>> indicates axis. Could you please give me suggessions about the correct way
>>> preparation of covarsconfig file for spinangle, it will be great help for
>>> me.
>>>
>>>
>>> Have a nice day,
>>> Thanks again,
>>> Maiti
>>>
>>
>>
>

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