[gmx-users] Re: how to calculate the force between two groups (Mark Abraham)

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 1 01:48:33 CET 2011

On 1/11/2011 5:40 AM, Tom wrote:
> Thanks Mark!
> It was actually what I did.
> mdrun -rerun  with well-chosen energy group exclusions only gives the 
> energy
> between certain pairs of group, not the forces.

Did you use nstfout to actually write the forces?

> g_traj gives the overall forces not the force between certain pair.

mdrun computes interactions as a loop over energy groups and writes only 
a single number for each component of the force on each atom in each 
time step. You can't decompose anything after the fact.

> Thanks a lot for any further idea to obtain the force for certain pair 
> of groups!

One can use tpbconv and trjconv to create a matching pair of subset .tpr 
and trajectory files for mdrun -rerun, but I do not think this is necessary.


> Tom
> On 31/10/2011 4:05 AM, Tom wrote:
> > Dear Gromacs Users,
> >
> > I have a question about how to ouput the force between two groups.
> >
> > Suppose the system consists of the groups: A, B, C and D.
> > I need the force only between the groups A and B.
> >
> > g_traj looks only to be able to report the overal forces and cann 
> not distiguish
> > the forces from different groups.
> >
> > Is there any cunning way to do it.
> >
> mdrun -rerun  with well-chosen energy group exclusions probably works
> for you.
> Mark 

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