<div>Hi!</div>
<div>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 file? </div>
<div>As per your suggestions I would be going with the PME so should the mdp file modified to incorporate the parameters below be sufficient?!!</div>
<div> </div>
<div>ns_type = grid<br>rlist = 1.0<br>rcoulomb = 1.0<br>rvdw = 1.4</div>
<div>vdwtype = cut-off</div>
<div>fourierspacing = 0.12</div>
<div>fourier_nx = 0</div>
<div>fourier_ny = 0</div>
<div>fourier_nx = 0</div>
<div>pme_order = 4</div>
<div>ewald_rtol = 1e-5</div>
<div>optimize_fft = yes</div>
<div>disre = simple<br>disre_weighting = equal</div>
<div> </div>
<div> </div>
<div>Thanks</div>
<div>Jayant James</div>