[gmx-users] HEME simulation

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 23 18:03:45 CEST 2007

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

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