<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">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><div>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<br></div>
</div><br></body></html>