Dear Justin Thank you For your Previous reply, For My system After First Shrinking Using Cut-off Value DPPC 18 perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat
Then I do the EM.During EM I need to use -maxwarn 1 option Otherwise I have got Error as follows in grompp If i use -maxwarn 1 then it runs Successfully May i use this -maxwan option in first Shrinking ? ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top -o 2KDQDPPCem.tpr Number of degrees of freedom in T-Coupling group rest is 19557.00 Largest charge group radii for Van der Waals: 1.201, 1.144 nm Largest charge group radii for Coulomb: 1.201, 1.144 nm WARNING 1 [file emdppc.mdp]: The sum of the two largest charge group radii (2.345197) is larger than rlist (1.200000) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 168x168x42, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.92 NOTE 2 [file emdppc.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Fatal error: Too many warnings (1), ./grompp_d terminated. If you are sure all warnings are harmless, use the -maxwarn option. Thanks In Advance -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
