**From:** Jim Phillips (*jim_at_ks.uiuc.edu*)

**Date:** Mon Feb 02 2004 - 13:27:10 CST

**Next message:**Neema Salimi: "Momenta output format"**Previous message:**Jim Phillips: "Re: How do we combine chains in the end"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

---------- Forwarded message ----------

Date: Mon, 2 Feb 2004 12:45:13 -0600 (CST)

From: Aleksei Aksimentiev

Hi Himanshu,

In order to compute the torque you need to record actual positions of the

atoms to which you apply the spring forces. This should be done after

your namd run is complete. You take the dcd trajectory, and extract the

radius-vector of all atoms subject to the force. Next, you need to compute

force. For that, you use the 2K(R-Rt(t)) formula, where R is the actual

position of the atom, Rt(t) is the position of the rotating template.

Ones you know all forces and radius vectors, you can compute the torque

as T=[RxF].

Alek

*> hi all -
*

*> referring to the rotating constraints feature in namd. We know
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*> that the force is 2K(R-X). Now R is the current reference position
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*> which should hence lie in the rotational circle in which we rotated the
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*> atom - and as we've already given the angular velocity of rotation we
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*> already know the current reference position at any time.
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*>
*

*> My problem is about X. Now though the manual doesn't say it - X should be
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*> the current position of the atom(i'm sorry if i'm wrong and ofcourse all
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*> these quantities are vectors).
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*>
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*> My problem is in calculating the torque which i've put on each atom.
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*> Though it appears easy to do - how can the torque be zero if i have put my
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*> spring constants so stiff that the atoms being rotated follow their
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*> reference point very closely.
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*>
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*> Now - i am sure that i am wrong somewhere - could you please point out
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*> where i am wrong - and hence how the torque applied on the atom
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*> calculated.
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*>
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*> thanks
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*>
*

*> himanshu
*

*> iit delhi
*

*>
*

**Next message:**Neema Salimi: "Momenta output format"**Previous message:**Jim Phillips: "Re: How do we combine chains in the end"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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