[gmx-users] restraining Ca2+ ion

jayant james jayant.james at gmail.com
Wed Jan 7 18:17:11 CET 2009

Thanks for your suggestions. In my protein there are two phosphorylated
serines (-vely charged) adjacent to each other on chain A and these
serines start to move towards the Ca2+ ion in chain B. It is only after a
while of them being close to each other that the Ca2+ starts popping off.
Also to modify the charges of the residues adjoining the Ca2+ ion, what file
should I be looking for to make these changes? would it be the topology
As per your suggestions I would be going with the PME so should the mdp file
modified to incorporate the parameters below be sufficient?!!

ns_type        =  grid
rlist              =  1.0
rcoulomb      =  1.0
rvdw             =  1.4
vdwtype        =  cut-off
fourierspacing = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nx      = 0
pme_order     = 4
ewald_rtol     =  1e-5
optimize_fft   = yes
disre            =  simple
disre_weighting     =  equal

Jayant James
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