Nikhil,
I had a similar problem, and was getting the same error. In my case the order of my atoms was different in my pdb/gro and my top/itp file. This made my system do a weird inversion, due to incorrect placement of atoms. And my energies were terrible.
Hope this helps,
TJ Mustard
On December 28, 2010 at 8:26 AM nikhil damle <[email protected]> wrote:
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
TJ Mustard
Email: [email protected]
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
