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