[gmx-developers] RasMol on Debian

[Mark Abraham]

Michael Bajomo wrote:
> Sir,
>  This is not a gromacs developer question but I am desperate and you are the
> only one that can help me. I learning to use gromacs as part on my project
> and I ran the Ribonuclease s-peptide tutorial on the gromacs website (
> www.gromacs.org <http://www.gromacs.org>). I modified the .mdp file so it
> runs for 1ns. When I check pressure using g_energy the average is
> 0.85barbut the RMSD is
> *345bar*. The .mdp file specifies 1bar and berendsen P-coupling. I don't
> know what I have done wrong. Any advice will be appreciated.
>  Thank you and kindest regards

This sort of question is a question about the use of gromacs, not the 
development of it, and should go to gmx-users, not gmx-developers. It 
also has nothing to do with your subject line of "RasMol on Debian".

An instantanous pressure (however you define it) will necessarily vary 
quite a lot during pressure-coupled simulation. A positive pressure 
value just means the system has a tendency to expand, and a negative 
value means the system will tend to contract. This is exactly what you 
should expect - the coupling is (effectively) a dynamic equilibrium with 
an infinite body with the reference pressure.

After a proper equilibration period, a P-coupled MD simulation should 
have an average pressure that is close to the reference pressure for the 
P-coupling. A value of 0.85 bar over a period of 1ns is suggestive that 
something is badly wrong with the system. A first thing to look at is 
the variation of pressure over time - if it's converging to 1 bar over 
the first part of the simulation then you need to treat that segment as 
the equilibration period and start measuring after you deem it 
equilibrated.

Usually some regime like
1) minimise energy after solvating,
2) equilibrate at constant V until T stabilises near the desired 
temperature for T-coupling,
3) equilibrate at constant P until P, T and hopefully the density are 
all reasonable, and finally
4) simulate
works.

Mark Abraham