[gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

[Justin Lemkul]

On 1/15/20 2:38 PM, ZHANG Cheng wrote:
> 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

Performance metrics are reported in the .log file from the run. Check 
there to see what is happening.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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