[gmx-users] SMD - reproducibility

Steven Neumann s.neumann08 at gmail.com
Fri Apr 26 11:47:31 CEST 2013

Dear Users,

I am running my puling simulations of ligand with constant velocity. First
I minimize and equilibrate my system:

grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
mdrun -s em.tpr -deffnm em
grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
mdrun -s nvt298.tpr -deffnm nvt298
grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
topol.top -o npt298.tpr
mdrun -s npt298.tpr -deffnm npt298

Then I run 10 pulling simulations with the same mdp file:

grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
mpiexec mdrun -s pull_1.tpr -deffnm pull_1


grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
mpiexec mdrun -s pull_10.tpr -deffnm pull_10

I get 3 different (but similar) profiles (Force vs time) with 10
simulations as some of them produce exactly the same results... In another
system with the same methodology I get 10 similar but different profiles. I
am wondering why in this case only 3 types are possible... Shall I try
grompp without -t npt.cpt ?


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