FOR GROMACS 5.1.xxx: !!!! 11.131, 11.132, 11.134, 11.136, 11.
140
gmx energy -b XX000 -e YY000 -nmol AAAA -fluct_props
gmx msd -f traj.trr -s production.tpr
gmx dipoles -f traj.trr -s production.tpr
gmx trjcat -f trajaft70.trr -o trajaft80.trr
gmx dipoles -f trajaft80.trr -s production.tpr
############################################################
cp *.pdb NI_40, cp *.itp, cp *.mdp, cp topol.top
vi topol.top CR, #molecules
The initial configuration is prepared as following:
Creation of the box and insertion of DMSO:
genbox -ci dmso.pdb -nmol 300 -box 4.861 4.861 4.861 -o initial.gro -try 1000 -p
topol.top
Addition of ions (if you want them):
genbox -cp initial.gro -ci chloride.pdb -nmol 20 -o initialions.gro -try 1000 -p
topol.top
genbox -cp initialions.gro -ci sodium.pdb -nmol 20 -o initialions.gro -try 1000 -p
topol.top
Adding water:
genbox -cp initialions.gro -ci spce.pdb -nmol 2700 -o initialwat.gro -try 1000 -p
topol.top
Check topol.top for correctness.
Minimisation:
###################################
grompp -f min.mdp -po minimise.mdp -c initialwat.gro -p topol.top -pp -o min.tpr
#########################################
mdrun -s min.tpr -v -c minimised.gro
Equilibration: Compile and then run
##################################
grompp -f eq.mdp -po eqnpt.mdp -c minimised.gro -p topol.top -pp -o equil.tpr
####################################
nohup mdrun -s equil.tpr -c equilfinal.gro -nt 8 -v &
##############
tail nohup.out
###################finished
mkdir RESCALE
cp equil.tpr RESCALE
cp state.cpt RESCALE
cp processed.top RESCALE
cp run.mdp RESCALE
###################
define = -DFLEXDMSO
integrator = md
tinit = 0
dt = 0.002
nsteps = 5000000
comm-mode = Linear
nstcomm = 100
comm-grps = system
nstxout = 2000
nstvout = 0
nstfout = 0
nstlog = 2000
cutoff-scheme = group
nstlist = 20
ns_type = grid
pbc = xyz
periodic-molecules = no
coulombtype = PME
rcoulomb = 1.4
rlist = 1.4
vdw-type = Cut-off
rvdw = 1.4
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
DispCorr = EnerPres
tcoupl = v-rescale
tc-grps = System
ref-t = 298.15
tau-t = 0.5
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
compressibility = 4.5e-5
tau-p = 2
ref-p = 1
constraints = all-bonds
constraint-algorithm= lincs
continuation = yes
###################################### cd RESCALE
gmx energy -b XX000 -e YY000 -nmol AAAA -fluct_props
gmx msd -f traj.trr -s production.tpr
gmx dipoles -f traj.trr -s production.tpr
gmx trjcat -f trajaft70.trr -o trajaft80.trr
gmx dipoles -f trajaft80.trr -s production.tpr
4 files are necessary equil.tpr, state.cpt, processed.top, run.mdp
grompp -f run.mdp -po prodrun.mdp -c equil.tpr -o production.tpr -t state.cpt -p
processed.top
nohup mdrun -s production.tpr -c final.gro -nt 8 -v &
make click 'ENTER' !! twice
check your run: tail nohup.out
exit
!!!! Radial distribution functions:
step 1: Make index file -
gmx make_ndx -f production.tpr -o index.ndx
a OW, a HW1, a OHM, q
g_rdf -f traj.trr -s production.tpr -n index.ndx -o grClClNaOWO1 -ng 4 -cn
gr_cnClClNaOWO1
3 3 4 13 15
g_rdf -f traj.trr -s production.tpr -n index.ndx -o grNaNaClOWO1 -ng 4 -cn
gr_cnNaNaClOWO1
4 4 3 13 15
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grClClNaOWO1 -cn
gr_cnClClNaOWO1
3 3 4 13 15, Ctrl D
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grNaNaClOWO1 -cn
gr_cnNaNaClOWO1
4 4 3 13 15, ctrl D
gmx make_ndx -f production.tpr -o index.ndx
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grOw_OwHw -cn gr_cnOw_OwHw
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grOw_OmHm -cn gr_cnOw_OmHm
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grOm_OwHw -cn gr_cnOm_OwHw
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grOm_OmHm -cn gr_cnOm_OmHm
