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
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