Dear GMXers, I'm simulating a SPC/E water box with the size of 4nm by 4nm by 4nm. The command "g_tune_pme" was used to find the optimal PME node numbers, Coulomb cutoff radius and grid spacing size.
The following command is used: g_tune_pme -np 24 -steps 5000 -resetstep 500 ... rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The simulation is done with no error. Below is the output: --------------------------- Line tpr PME nodes Gcycles Av. Std.dev. ns/day PME/f DD grid 0 0 12 2813.762 187.115 9.604 0.361 4 3 1 1 0 11 2969.826 251.210 9.112 0.510 13 1 1 2 0 10 2373.469 154.005 11.385 0.445 2 7 1 3 0 9 2129.519 58.132 12.665 0.601 5 3 1 4 0 8 2411.653 265.233 11.248 0.570 4 4 1 5 0 7 2062.770 514.023 13.490 0.616 17 1 1 6 0 6 1539.237 89.189 17.547 0.748 6 3 1 7 0 0 1633.318 113.037 16.548 - 6 4 1 8 0 -1( 4) 1330.146 32.362 20.276 1.050 4 5 1 --------------------------- The optimal -npme is 4. It seems to me that the "Std. dev" is too huge. Can anyone tell me the meaning of "Gcycles Av." and "Std. dev" and their relations to the accuracy of "ns/day"? Another question: I tried g_tune_pme -np 24 -steps 1000 -resetstep 100 ... (the default value of g_tune_pme) rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 The optimal -npme is 6, different from "-npme=4" as obtained with big "-nsteps". Should I increase "-nsteps" even more to get better estimate, or what else parameters should I try? Do let me know if the questions are not made clear. Thank you. Best, Yanbin
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