[gmx-users] Forces on atom which is shifted out of the minimum

Mark Abraham mark.abraham at anu.edu.au
Tue Jun 1 19:54:01 CEST 2010

----- Original Message -----
From: Sebastian Waltz <sebastian.waltz at physik.uni-freiburg.de>
Date: Tuesday, June 1, 2010 21:33
Subject: [gmx-users] Forces on atom which is shifted out of the minimum
To: gmx-users at gromacs.org

> Hi all together,
> I need to calculate the first derivative of the force or
> the second derivative of the potential. Therefore I need
> the force on an atom which is shifted out of the minimum
> along the constrained bond direction for each time step.
> There in the Gromacs code is the force actually calculated?
> Does someone has any idea where to start?    

Since GROMACS doesn't use the second derivatives (except perhaps in some implementations of EM), it's not routinely calculated.

If you want to calculate them, then you will need to look at modifying a whole pile of code (but first see if anything useful is done with the EM integrators). Bonded and non-bonded interactions are treated differently. Making the non-bonded code calculate and output these second derivatives with any speed will be serious work.

My usual observation is that you'll be hopelessly lost doing such far-reaching changes without having gotten a debugger and stepped through a GROMACS run on a toy example.


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