[gmx-users] Energy minimization 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101228/af806330/attachment.html>