Hello i am a beginner in Gromacs.
I am using MPI Program. I want to run last production command of md simulation
mpirun -np $NUM_CPU gmx mdrun -ntomp 1
set init = step3_input
set mini_prefix = step4.0_minimization
set equi_prefix = step4.1_equilibration
set prod_prefix = step5_production
set prod_step = step5
Minimization
In the case that there is a problem during minimization using a single precision of GROMACS, please try to use
a double precision of GROMACS only for the minimization step.
gmx grompp -f {mini_prefix}.mdp -o {mini_prefix}.tpr -c {init}.gro -r {init}.gro -p topol.top -n index.ndx -maxwarn -1
gmx_d mdrun -v -deffnm ${mini_prefix}
Equilibration
gmx grompp -f {equi_prefix}.mdp -o {equi_prefix}.tpr -c {mini_prefix}.gro -r {init}.gro -p topol.top -n index.ndx
gmx mdrun -v -deffnm ${equi_prefix}
Production
set cnt = 1
set cntmax = 10
while ( {cnt} <= {cntmax} )
@ pcnt = {cnt} - 1
set istep = {prod_step}{cnt}
set pstep = {prod_step}${pcnt}
if ( ${cnt} == 1 ) then
set pstep = ${equi_prefix}
gmx grompp -f ${prod_prefix}.mdp -o ${istep}.tpr -c ${pstep}.gro -p topol.top -n index.ndx
else
gmx grompp -f ${prod_prefix}.mdp -o ${istep}.tpr -c ${pstep}.gro -t ${pstep}.cpt -p topol.top -n index.ndx
endif
gmx mdrun -v -deffnm ${istep}
@ cnt += 1
end
how can i run a simulation of 50ns .
what does this -ntomp1 means (written in first line of code)??