[gmx-users] equilibration

Arvid Soederhaell arvid at fmp-berlin.de
Fri Aug 8 09:39:00 CEST 2003

Hi all
I am trying to equilibrate a membrane-peptide-water-ion system but it
doesn't work. Gromacs is quite new to me so the questions might be stupid.
The system should already be quite well equilibrated since it comes from
dynamics run using amber. The only thing that is done is making a new
periodic box and adding hydrogens. 

I have tested to do a steepest descen minimization and the error message
in the .log file is:  
Stepsize too small (6.10352e-07 nm)Converged to machine precision, 
but not to the requested precision (1) 
You might need to increase your constraint accuracy, or turn off
constraints alltogether (set constraints = none in mdp file) 

Steepest Descents did not converge in 15 steps
  Potential Energy = nan Maximum force:  1.45952e+10
--------------------------------------------------------------------- I
have set nsteps = 1000, emtol = 1.0 and emstep = 0.01. I really don't get
what the "Stepsize too small (6.1035" etc. means? I have also set the
constraints = none, but nothing changes. 

When I try to make a dynamics simulation instead the system explodes
immediately and I get the following error message after 9 steps: 
Fatal error: ci = -2147483648 should be in 0 .. 1880 [FILE nsgrid.c, LINE
When I look at the dynamics trajectory all atoms are out of the box in 2
steps. Even when I use dt = 0.001. 

A question that will be a problem later: I would like to scale the
temperature of the peptide, the lipids and water+ions separately. How
should I formulate this in the .mdp file? (How to put water and ions in
the same group?)
tcoupl  = Berendsen 
tc_grps = Protein DPPC (SOL Cl)   ????? 
tau_t   =   0.1    0.1   0.1 
ref_t   =    30     30    30 

The topology file looks like this (Note that in the [molecules] section
I have commented away the "Protein 1" line. If I keep thath line, grompp 
complains and count the number of atoms in the protein twice!!?? The
rw-conn.itp file describes the peptide.):
#include "ffgmx.itp"  
#include "lipid.itp"  
#include "dppc.itp"  
#include "rw-conn.itp" 
#include "ions.itp" 

#ifdef FLEX_SPC 
#include "flexspc.itp"  
#include "spc.itp"  

[ system ]  
; name 
PMWI (Peptide Membrane Water Ion) 

[ molecules ] 
; name number 
;Protein 1 
DPPC 64 
SOL 2463 
Cl 3

Thanx in advance 
    Arvid Soderhall

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