[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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