[gmx-users] equilibration

Mehmet Suezen mehmet at suezen.org
Fri Aug 8 10:15:01 CEST 2003

Before trying to minimize, running in NVT ensemble 
some time suitable to your system, might be helpful.
What was the previous ensemble in your dynamic run?
Also changing your geometry of PBC would change 
all the previous coordinates, isn't it? What
about integration time step.


>-- Original Message --
>From: Arvid Soederhaell <arvid at fmp-berlin.de>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] equilibration
>Reply-To: gmx-users at gromacs.org
>Date: Fri, 8 Aug 2003 09:38:36 +0200 (MEDT)
>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
>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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>gmx-users at gromacs.org
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Mehmet Suzen  AMInstP

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