Dear all, 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. The enery minimaization was run without problem with the results: Steepest Descents converged to Fmax < 2000 in 84 steps Potential Energy = -1.5738966e+05 Maximum force = 1.8819653e+03 on atom 77 Norm of force = 9.0745400e+03 When I try to run position restraint dynamic the process end with error as follow: 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. 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: FE 1.31 NA -0.78 NB -0.81 NC -0.8 ND -0.79 CHA 0.33 HHA 0.0 C1A 0.24 C2A 0.04 C3A 0.06 C4A 0.22 CMA 0.03 CAA 0.02 CBA 0.07 CGA 0.5 O1A -0.18 O2A -0.46 CHB 0.04 HHB 0.0 C1B 0.22 C2B 0.06 C3B -0.02 C4B 0.22 CMB 0.03 CAB 0.07 CBB -0.01 CHC 0.05 HHC 0.0 C1C 0.22 C2C 0.06 C3C -0.03 C4C 0.22 CMC 0.02 CAC 0.08 CBC -0.01 CHD 0.05 HHD 0.0 C1D 0.23 C2D 0.05 C3D 0.04 C4D 0.24 CMD 0.03 CAD 0.0 CBD 0.0 CGD 0.41 O1D -0.61 O2D -0.66 H1A 0.0 What should I do? Thanks a lot Send instant messages to your online friends http://uk.messenger.yahoo.com
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
