nikhil damle 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 !
Nearly 87,000 atoms are being assigned parameters that do not belong to them.
The order of the [molecules] directive and the coordinate file must match.
Otherwise, grompp (and then mdrun) will think that water is protein, and protein
residues are other residues, etc. I would be a fan of making -maxwarn a hidden
option; it really should not be used unless one knows the exact consequences of
doing so.
-Justin
Regards,
Nikhil
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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