<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div><div>Hi,<br>
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. <br>
<br>
System Details:<br>
# Atoms = 4488 (# Res = 582)<br>
octahedron box with d = 0.9<br>
Solvent (spce water model) density = 1050.6 g/L (During monomer MD it was 1048.86 g/L)<br>
<br>
System subjected to energy minimisation, <br>
Only warning arising during grompp:<br>
-------------------------------------------------------<br>
WARNING 1 [file dimer.top, line 46]:<br>
86974 non-matching atom names<br>
atom names from dimer.top will be used<br>
atom names from neutral.pdb will be ignored<br>
-------------------------------------------------------<br>
This was neglected using -maxwarn option
and contd...<br>
Error during minimisation run (mdrun):<br>
-------------------------------------------------------<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+03<br>
Number of steps = 50000<br>
Step= 14, Dmax= 1.2e-06 nm, Epot= 7.04150e+23 Fmax= inf, atom= 37<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 1000<br>
<br>
Double precision normally gives you higher accuracy.<br>
<br>
writing lowest energy coordinates.<br>
<br>
Steepest Descents converged to machine precision in 15 steps,<br>
but did not reach the requested Fmax < 1000.<br>
Potential Energy = 6.9065950e+23<br>
Maximum force = inf on atom
37<br>
Norm of force = inf<br>
-----------------------------------------------------<br>
<br>
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<br>
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.)<br>
<br>
What could possibly go wrong ? Could it be really the step size or precision although I do not think so !<br>
<br>
Regards,<br>
Nikhil</div>
</div>
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