[gmx-users] an error for mdrun

[Mark Abraham]

Hi,

Why should it be stable?

Mark

On Sun, Jun 12, 2016 at 4:01 PM <15110700076 at fudan.edu.cn> wrote:

>
>
> Hello,
>      everyone.
>      I recently created a system for PDE2 , a protein containing two ions
> (Zn and Mg) in its pocket. The distance between the  two ions is about 3.9
> Å. Thus the strong   electrostatic force
>  between them made the system blow up. One part of my .mdp parameters are
> here:
>
> ;neighbor searching
>
> nstlist         =10
>
> ns_type         =grid
>
> pbc             =xyz
>
> rlist           =1.4
>
> ;electrostatics
>
> coulombtype     =PME
>
> rcoulomb        =1.4
>
> ;vdw
>
> vdwtype         =Cut-off
>
> rvdw            =1.4
>
> dispCorr        =EnerPres
>
> ;Ewald
>
> fourierspacing  =0.1
>
> pme_order       =4
>
> ewald_rtol      =1e-5
>
>
> How can I do to overcome it? thank you！
>
>
> Best wishes,
>
> ------------------------------------------------------------
>
> Qing Liu
>
> Fudan Univ.
>
> E-mail: 15110700076 at fudan.edu.cn
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