[gmx-users] Force output

[ilona.baldus at bioquant.uni-heidelberg.de]

I think this one can help you:

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000306

You can download a code that gives you the forces from the following website:

  http://projects.eml.org/mbm/website/fda_gromacs.htm

Ilona


Quoting Avisek Das <avisek at stanford.edu>:

> Dear GROMACS developers and users,
>
>                   I have a question regarding GROMACS force output.   
> I need the total force on each atom at every timestep in a constant   
> temperature MD trajectory. I am using the Nose-Hoover thermostat for  
>  constant temperature simulations. I know that by using the  
> 'nstfout'  keyword in the .mdp file I can tell GROMACS to output  
> forces in the  trajectory (.trr) file. Now my question is  what  
> exactly is written  in the output file as "force" when I use the  
> above mentioned option.
>
>                   I understand that at first this question may seem   
> a little strange and unnecessary, since everybody knows what a force  
>  is, but in the context of Nose-Hoover dynamics there is a slight   
> chance of potential confusion as discussed below. The force   
> information is very crucial for our subsequent analysis, that is why  
>  we wanted to make sure that we know exactly what is being printed   
> when one uses the 'nstfout'  keyword.
>
>                  Total force on a particle can be interpreted as   
> either the negative gradient of the total potential energy with   
> respect to the position of the atom in question OR the instantaneous  
>  rate of change of momentum of the atom. Now for normal Hamiltonian   
> dynamics both of these definitions will give the same number but for  
>  the Nose-Hoover dynamics they will be different. Because in the    
> Nose-Hoover equations the rate of change of momentum of an atom is a  
>  sum of two terms, first term is the negative gradient of total   
> potential and the second term is momentum of the particle multiplied  
>  by a thermostat parameter. So, in Nose-Hoover equation  
> instantaneous  rate of change of momentum is NOT equal to the  
> negative gradient of  the potential with respect to the atom position.
>
>                  In the light of above discussion can anyone please   
> tell me when GROMACS prints forces in the trajectory file during a   
> Nose-Hoover dynamics, which quantity does it print? Is it the   
> negative gradient of the total potential with respect to the atom   
> position OR the total instantaneous rate of change of momentum which  
>  includes an extra term?
>
>
> Thanks a lot,
> Avisek
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