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: 15110700...@fudan.edu.cn
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