[gmx-users] Energy minimisation query

[nikhil damle]

Hi,
I am trying to simulate a dimeric structure and I have already simulated its 
monomeric form. I use exactly same parameters which i use for monomer during 
dimer minimisation in solvent. 


System Details:
# Atoms = 4488 (# Res = 582)

octahedron box with d = 0.9
Solvent (spce water model) density = 1050.6 g/L (During monomer MD it was 
1048.86 g/L)

System subjected to energy minimisation, 
Only warning arising during grompp:
-------------------------------------------------------
WARNING 1 [file dimer.top, line 46]:
  86974 non-matching atom names
  atom names from dimer.top will be used
  atom names from neutral.pdb will be ignored
-------------------------------------------------------
This was neglected using -maxwarn option and contd...
Error during minimisation run (mdrun):
-------------------------------------------------------
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=   14, Dmax= 1.2e-06 nm, Epot=  7.04150e+23 Fmax=         inf, atom= 37
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  6.9065950e+23
Maximum force     =            inf on atom 37
Norm of force     =            inf
-----------------------------------------------------

1) I thought that the box size is too small so that dimer is not able to move at 
all and hence the energy is too high. But I am getting same error even if box 
size is increased to 2.0 nm
2) I checked my initial structure and even the neutralised structure post 
solvation only to find that it is not broken. (My system has a missing loop 
which I have modeled using modeler9v8 and then subjected it to MD in solvent.)

What could possibly go wrong ? Could it be really the step size or precision 
although I do not think so !

Regards,
Nikhil


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