[gmx-users] large pressure

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jul 10 02:05:34 CEST 2009

Shuangxing Dai wrote:
> Hi, all,
>     I was wondering why I got large pressure after energy 
> minimization. In MD, the pressure and pressure tensor is defined like ( 
> equation 4.151 in manual):
>                 P=2*(E_kinetic  +  W)/(3*V), V is volume and W is Virial.
> I run a simple system, fcc gold with LJ potential to check the pressure 
> after energy minimization.  I got:

There are no velocities, so whatever is computed here is not the pressure.

>  Pressure (bar)
>     8.75158e+03
> Steepest Descents converged to Fmax < 1 in 1 steps
> Potential Energy  = -1.4870625e+03
> Maximum force     =  2.2925207e-05 on atom 1606
> Norm of force     =  7.9803776e-06  
> The force is very small and the energy minimization finished in 1 steps, 
> since all the atoms are at equilibrium. So I was wondering why I got 
> this huge pressure. And in a lot of simulations, I found huge pressure 
> after energy minimization. Even in free energy tutorial on Wiki, I found 
> large pressure as larege as 1 GPa. 

See http://oldwiki.gromacs.org/index.php/Pressure

> After energy minimization, the forces 
> are very small and no velocity, so the pressure should be close to zero.
> Anyone has any idea about this?

I guess it should not be computed.

> PS: Why the forces in traj.trr are all zeros?

EM doesn't write forces.


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