[gmx-users] Coulomb LR - PME vs. Cut-off

Marc Charendoff mcharend at sbcglobal.net
Tue Apr 6 17:15:48 CEST 2010


     I am currently running MD on a protein-ligand complex centered in an (approx) 70.0 Angstrom ^3 water box with sodium counterions. I have run  1.0 ns simulations under two different conditions. The first condition with coulombtype "cut-off" I have run to perform LIE calcs as I have read PME will cause undesired artifacts. These runs tend to be unstable though with only varying success on obtaining completed production runs before box collapses. However, when I run under condition 2 (PME) I find that there is no problem at all, though I cannot then run g_lie (obviously). Would creating a bigger solvent box help in making the use of  cut-offs more stable? Is there not a preferred ratio of rcoulomb distance to some solvent box dimension that might alleviate this issue? Otherwise, what is it about PME exactly that creates issues for g_lie? Is there a way around it? Any guidance would be appreciated.

Regards, Marc

Condition 1

ns_type = grid
pbc = xyz
rlist = 0.9
coulombtype = cut-off
rcoulomb = 1.2
vdwtype = cut-off
rvdw = 1.4
Condition 2
 ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
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