# Evaluate Work for Targeted Molecular Dynamics Simulations

From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Aug 15 2012 - 16:08:52 CDT

Dear all,
In TMD the force on each atom is given by the gradient of the
potential; [image:
$\displaystyle U_{TMD} = \frac{1}{2} \frac{k}{N} \left[ RMS(t) - RMS^*(t) \right]^2$]
The TMD output consists of lines of the form:

*TMD ts targetRMS currentRMS.*

So....

I plan to evaluate the total work applied in the TMD simulation as

*W=sum_along_path( F*delta_X )*

where

*F(i)=k ( currentRMS(i) - targetRMS(i) )

delta_X(i)=**currentRMS(i+1) - currentRMS(i)

i *is the TMD step number (or output number)*.

*Did anyone have performed work calculations in TMD before ? If so are
there any source/publication/suggestions I can refer to ?

Do you think it makes sense to evaluate the work values as I indicated
above? Are there any problems in terms on how I interpret the TMD output
and use them to evaluate work values.

Best,

Mert
*

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