[gmx-users] energy minimization_note
Atila Petrosian
atila.petrosian at gmail.com
Wed Jul 18 17:35:33 CEST 2018
Dear gromacs users,
I am doing md simulation of cnt + drug + water molecules. The em.mdp file
is follows:
integrator = steep
nsteps = 50000
emtol = 10
emstep = 0.01
ns_type = grid
rlist = 1.0
coulombtype = PME
Cutoff-scheme = Verlet
vdwtype = Cut-off
rcoulomb = 1.0
rvdw = 1.0
constraints = none
periodic_molecules = yes
---------------------------------------------------
After using ( gmx_mpi grompp -f em_vac.mdp -c complex.gro -p topol.top -o
em_vac.tpr),
NOTE 1 [file em_vac.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing.
-----------------------------------------------------
Are these parameters true?
Which changes I should consider in this mdp file to have not this note?
Which cut-off is appropriate?
Best,
Atila
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