[gmx-users] HEME simulation

[gromacs user]

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
 
 
 
 
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