[gmx-users] HEME simulation

[David van der Spoel]

gromacs user wrote:
> 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:
> 
> 
check your energy components. are the bonds and angles low enough (this 
is in the minimization). How do the values differ in the dynamics?

-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se