Optimizing md run for a 10 to 50 ns simulation

User discussions
1

GROMACS version:2020.4
GROMACS modification: Yes/No
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hello,
I need advice from expert users.
How should we optimize the md run parameters for a biomolecular protein-ligand complex >400000 atoms to carry out final md run for 10 to 50 ns. The steps are enclosed herewith for a 10 ns simulation which has worked well but rmsd analysis after md run is in range of 5.0 Angstrom

dt=0.002
nsteps=5000000
nstxtcout=5000
nstvout=5000
nstfout=5000
nstcalcenergy=100
nstenergy=1000
nstlog=1000
and a verlett cutoff was applied.
Your inputs are much appreciated to save the computational time and space.
is it possible to do 10, 20 and 50 ns simulation is steps? continuing from previous steps as input?

many thanks for your advice in advance

2

Hi,

to extend a simulation run, one can generate a new tpr file using gmx convert-tpr (with options -extend , -until or -nsteps), and restart the simulation in the same working directory, gmx mdun will read the starting point using the checkpoint files ( .cpt).
(look also at other posts on “restrarting” a simulation
Best regards
Alessandra

3

I was wondering if I can modify the script to run it as 1 commnd?
set cnt=1
set cntmax=10

while ({cnt} <= {cntmax})

if ( ${cnt} == 1 ) then

gmx grompp -f step5_production.mdp -o step5_${cnt}.tpr -c step4.1_equilibration.gro -p topol.top

gmx mdrun -v -deffnm step5_${cnt}

else

@ pcnt = ${cnt} - 1

@ new_step = ${cnt} * 1000000

sed -e “s/1000000/{new_step}/g” step5_production.mdp > step5_production_{cnt}.mdp

gmx grompp -f step5_production_{cnt}.mdp -o step5_{cnt}.tpr -c step5_${pcnt}.gro -p topol.top

gmx mdrun -v -deffnm step5_${cnt}

endif

@ cnt += 1

end