[gmx-users] Error during minimization

Chris Neale chris.neale at utoronto.ca
Tue Jan 5 20:00:16 CET 2010

Hi Nisha,

you say "And it runs minimization with bad contact errors", but I don't see any indication of that error message here. 
Is it perhaps that your EM exits early and then your MD throws an error? In any event, please post complete error information
as output by gromacs.


-- original message --

I have a question regarding the simulations that I am running. I tried  
creating a pdb file with one methane and water molecules, but the  
system keeps showing 'bad contact' error when I run the minimization  
step and I don't understand what I am doing wrong.

  This is my methane file :

TITLE     methane  in water
CRYST1   33.010   33.010   33.010  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  CH4 CH4     1      19.520  25.090  16.410  1.00  0.00

So I use this file and run editconf -f methane1.pdb -o box.pdb -bt  
cubic. This creates a
box with volume of around 35 nm^3

Then I add water molecules using :

genbox -cp box.pdb -cs spc216 -o methwa.pdb -p topol.top

This adds around 1191 water molecules to the existing methane file. So  
my box is now
(33.010 33.010 33.010 with total 1192 molecules). Then I run  
minimization on this system
using minim.mdp as follows:

integrator        = steep
emtol                = 1.0
nsteps                = 100
nstenergy        = 10
nstxtcout        = 10
xtc_grps        = CH4 SOL
energygrps        = CH4 SOL
nstlist                = 5
ns_type                = simple
rlist                = 1.0
coulombtype        = cut-off
rcoulomb        = 1.0
rvdw                = 1.0
constraints        = none
pbc                = no

grompp -f minim.mdp -c methwa.pdb -p topol.top -v
  mdrun -v

And it runs minimization with bad contact errors and this is the result I get:
Steepest Descents converged to machine precision in 32 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -4.9481789e+04
Maximum force     =  3.2827865e+06 on atom 500
Norm of force     =  6.9951227e+04

Any suggestions?


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