I have a nearly identical run using the "VERSION 2019.3" compared to my previous "VERSION 5.1.1". Everything during the preparation is the same except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and production run, respectively.
Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be processed in the "VERSION 2019.3", while 200 ps can be achieved in the "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I can do in the "VERSION 2019.3" so as to accelerate the MD? I follow Justin's tutorial at http://www.mdtutorials.com/gmx/lysozyme/index.html The commands I used are listed below. gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce -inter -ignh -merge interactive gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL -nn 31 -neutral -conc 0.05 (Afterwards, using the HPC to run) gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr gerun mdrun_mpi -v -deffnm em gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro gerun mdrun_mpi -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro gerun mdrun_mpi -deffnm npt gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro gmx mdrun -deffnm md_0_1 -cpi -append -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.