Dear all,<br> <br> I am trying to run a simulation of the interaction between two HEME in water. I have done it without problem, but when I use the calculated charge of HEME atoms from ab initio calculation I have problem.<br> <br> The enery minimaization was run without problem with the results:<br> <br> Steepest Descents converged to Fmax < 2000 in 84 steps<br> Potential Energy = -1.5738966e+05<br> Maximum force = 1.8819653e+03 on atom 77<br> Norm of force = 9.0745400e+03<br> <br> When I try to run position restraint dynamic the process end with error as follow:<br> <br> <br> <br> t = 1.108 ps: Water molecule starting at atom 10423 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates.<br> <br> <br> I checked the simulation and I see some of atoms are transfered to the out of the box. I reduced timestep and changed box type and
coulombtype and deleted some water, but I didn t have any result. Also, the charge in my topology file is as follow:<br> <br> FE 1.31<br> NA -0.78<br> NB -0.81<br> NC -0.8<br> ND -0.79<br> CHA 0.33<br> HHA 0.0<br> C1A 0.24<br> C2A 0.04<br> C3A 0.06<br> C4A 0.22<br> CMA 0.03<br> CAA 0.02<br> CBA 0.07<br> CGA 0.5<br> O1A -0.18<br> O2A -0.46<br> CHB 0.04<br> HHB 0.0<br> C1B 0.22<br> C2B 0.06<br> C3B -0.02<br> C4B 0.22<br> CMB 0.03<br> CAB 0.07<br> CBB -0.01<br> CHC 0.05<br>
HHC 0.0<br> C1C 0.22<br> C2C 0.06<br> C3C -0.03<br> C4C 0.22<br> CMC 0.02<br> CAC 0.08<br> CBC -0.01<br> CHD 0.05<br> HHD 0.0<br> C1D 0.23<br> C2D 0.05<br> C3D 0.04<br> C4D 0.24<br> CMD 0.03<br> CAD 0.0<br> CBD 0.0<br> CGD 0.41<br> O1D -0.61<br> O2D -0.66<br> H1A 0.0<br> <br> <br> What should I do?<br> <br> Thanks a lot<br> <br> <br> <br> <p> Send instant messages to your online friends http://uk.messenger.yahoo.com