dips -o manuscript.ps manuscript.
dvi
ps2pdf manuscript.ps manuscript.pdf
$$$$$ 4.6 $$$$$
The initial configuration is prepared as following:
Creation of the box:
vi topol.top
genbox -ci methanol.pdb -nmol 3705 -box 6.5 6.5 6.5 -o initial.gro -try 1000 -p
topol.top
Addition of ions (if you want them):
genbox -cp initial.gro -ci chloride.pdb -nmol 8 -o initialions.gro -try 1000 -p
topol.top
genbox -cp initialions.gro -ci sodium.pdb -nmol 8 -o initialions.gro -try 1000 -p
topol.top
Adding water:
genbox -cp initialions.gro -ci tip4p.pdb -nmol 1 -o initialwat.gro -try 1000 -p
topol.top
Check topol.top for correctness.
Minimisation:
###################################
grompp -f min.mdp -po minimise.mdp -c initialions.gro -p topol.top -pp -o min.tpr
#########################################
mdrun -s min.tpr -v -c minimised.gro
###################################
Equilibration: Compile and then run
##################################
grompp -f eq.mdp -po eqnpt.mdp -c minimised.gro -p topol.top -pp -o equil.tpr
nohup mdrun -s equil.tpr -c equilfinal.gro -nt 8 -v &
grompp -f run.mdp -po prodrun.mdp -c equil.tpr -o production.tpr -t state.cpt -p
processed.top
nohup mdrun -s production.tpr -c final.gro -nt 8 -v &
$$$$$$$$ 5.1 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
$$$$$$$$$$$$$$$$$$$$$$$$
gmx insert-molecules -ci methanol.pdb -nmol 3285 -box 6.5 6.5 6.5 -o initial.gro -
try 1000
gmx insert-molecules -f initial.gro -ci chloride.pdb -nmol 15 -o initialions.gro -
try 1000
gmx insert-molecules -f initialions.gro -ci sodium.pdb -nmol 15 -o initialions.gro
-try 1000
gmx insert-molecules -f initialions.gro -ci spce.pdb -nmol 3699 -o initialwat.gro -
try 1000
gmx grompp -f min.mdp -po minimise.mdp -c initialions.gro -p topol.top -pp -o
min.tpr
gmx mdrun -s min.tpr -v -c minimised.gro
gmx grompp -f eq.mdp -po eqnpt.mdp -c minimised.gro -p topol.top -pp -o equil.tpr -
maxwarn 1
nohup gmx mdrun -s equil.tpr -c equilfinal.gro -nt 8 -v &
gmx grompp -f run.mdp -po prodrun.mdp -c equil.tpr -o production.tpr -t state.cpt
-p processed.top
nohup gmx mdrun -s production.tpr -c final.gro -nt 8 -v &
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
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#mkdir RESCALE -- cp processed.top RESCALE/ -- cp equil.tpr RESCALE/ -- cp
run.mdp RESCALE/ -- cp state.cpt RESCALE/ -- cd RESCALE
# vi 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 &
5.1 gmx grompp -f run.mdp -po prodrun.mdp -c equil.tpr -o production.tpr -t
state.cpt -p processed.top
5.1 nohup gmx mdrun -s production.tpr -c final.gro -nt 8 -v &
################################################## RESTART #################
EDITAR run.mdp as you can see below:
Cambiar: tinit = 0 (from 0 ns till 10ns)
A.. : tinit = 10000 (from 10 ns till 20 ns)
THEN:
grompp -f run.mdp -c production.tpr -o production.tpr -t state.cpt -p processed.top
and
nohup mdrun -s production.tpr -c final.gro -nt 8 -v &
AND THATS IT !
BEFORE RESTART COLLECT DATA:
If the run finished (check it by tail nohup.out) then:
g_energy -b 0 -e 10000 -nmol 3000 -fluct_props
................
1 2 3 4 5 6 7 8 9 10 11 16 17 18 19 20
......................... then take intomouse and save as a1.dat
# FOR SYSTEM
g_dipoles -f traj.trr -s production.tpr
save epsilon into a1.dat
g_msd -f traj.trr -s production.tpr -beginfit 1000 -endfit 5000
save result for WATER into a1.dat
NOW for methanol:
# First we need an index file with indices of molecules.
We have 2700 MeO molecules (indices of MeO molecules are from 1 to 2000)
# To generate this file we use the following command:
g_select -s production.tpr -select "atomnr 1 to 2700" -on _ndx.ndx
# Then we compose a trajectory file made of centers of mass of METH molecules
g_traj -f traj.trr -oxt meth.xtc -fp -s production.tpr -n _ndx.ndx -mol
# Now we can calculate MSD based on the new trajectory file
g_msd -f meth.xtc -s production.tpr -o msd_meth.xvg -beginfit 1000 -endfit 5000 -n
_ndx.ndx
Save result into a1.dat
###########################
!!! Radial distribution functions:
step 1: Make index file -
make_ndx -f production.tpr -o index.ndx
a OW, a HW1, a O, q OHM
g_rdf -f traj.trr -s production.tpr -n index.ndx -o grClClNaOwOm -ng 4 -cn
gr_cnClClNaOwOm
g_rdf -f traj.trr -s production.tpr -n index.ndx -o grNaNaClOwOm -ng 4 -cn
gr_cnNaNaClOwOm
g_rdf -f traj.trr -s production.tpr -n index.ndx -o grOwOw -ng 1 -cn gr_cnOwOw
g_rdf -f traj.trr -s production.tpr -n index.ndx -o grOmOm -ng 1 -cn gr_cnOmOm
gmx make_ndx -f production.tpr -o index.ndx
a OW, a HW1, a O, q OHM
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grClClNaOwOm -cn
gr_cnClClNaOwOm
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grNaNaClOwOm -cn
gr_cnNaNaClOwOm
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grOwOw -cn gr_cnOwOw
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grOmOm -cn gr_cnOmOm
; Ctrl+D
gmx rdf -f traj.trr -s production.tpr -n index.ndx -o grNaNaClOWH -cn
gr_cnNaNaClOWH
; Ctrl+D
##################################################################
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 &
g_energy -b 50000 -e 60000 -nmol 3080 -fluct_props
1 2 3 4 5 6 7 8 9 10 12 13 16 17 18 19 20
trjcat -f traj.trr traj.trr -o trajaft60.trr
rm
g_dipoles -f traj.trr -s production.tpr
g_msd -f traj.trr -s production.tpr -beginfit 5000 -endfit 10000
g_select -s production.tpr -select "atomnr 1 to 3000" -on _ndx.ndx
g_traj -f traj.trr -oxt meth.xtc -fp -s production.tpr -n _ndx.ndx -mol
g_msd -f meth.xtc -s production.tpr -o msd_meth.xvg -beginfit 1000 -endfit 5000 -n
_ndx.ndx
vi run.mdp
grompp -f run.mdp -c production.tpr -o production.tpr -t state.cpt -p processed.top
nohup mdrun -s production.tpr -c final.gro -nt 8 -v &
tail nohup.out
#############################################################
gmx energy -b 30000 -e 20000 -nmol 3315 -fluct_props
5 2 3 4 5 6 7 8 9 10 11 16 17 18 19 20
gmx trjcat -f trajaft50.trr traj.trr -o trajaft70.trr
gmx dipoles -f traj.trr -s production.tpr
gmx msd -f traj.trr -s production.tpr -beginfit 5000 -endfit 10000
gmx select -s production.tpr -select "atomnr 1 to 3000" -on _ndx.ndx
gmx traj -f traj.trr -oxt meth.xtc -fp -s production.tpr -n _ndx.ndx -mol
gmx msd -f meth.xtc -s production.tpr -o msd_meth.xvg -beginfit 1000 -endfit 10000
-n _ndx.ndx
vi run.mdp
gmx grompp -f run.mdp -c production.tpr -o production.tpr -t state.cpt -p
processed.top
nohup gmx mdrun -s production.tpr -c final.gro -nt 8 -v &
gmx clustsize -f trajaft40.trr -s production.tpr -o cluster.xpm -nc nclust.xvg -
cut 0.290 -nskip 50 -mc maxclust.xvg -ac avclust.xvg -hc histo-clust.xvg -n
index.ndx
g_clustsize -f trajaft90.trr -s production.tpr -o cluster.xpm -nc nclust.xvg -cut
0.285 -nskip 50 -mc maxclust.xvg -ac avclust.xvg -hc histo-clust.xvg -n index.ndx
selec IONS
# ==== HYDROGEN BONDS ====
# g_hbond analyses all hydrogen bonds existing between two groups of atoms (which
# must be either identical or non-overlapping) or in specified donor-hydrogen-
acceptor
# triplets using the D−A distance and D−H−A angle criterions.
# You choose two groups. One representing donor group (O14-H15) and another is
acceptor group (OAD).
g_select -s run.tpr -select "name O14,H15" -on _ndx1.ndx # select indices of
sites belonging to donor group
g_select -s run.tpr -select "name OAD" -on _ndx2.ndx # select indices of
sites belonging to acceptor group
cat _ndx1.ndx _ndx2.ndx >_ndx.ndx
echo "0 1" | g_hbond -r 0.34 -f mix_run.trr -s run.tpr -n _ndx.ndx -num O14-
H15_OD_hbnum.xvg
rm -f _ndx1.ndx _ndx2.ndx _ndx.ndx
##########################################
g_select -s production.tpr -select "name OW,HW1,HW2" -on _ndx1.ndx
g_select -s production.tpr -select "name O" -on _ndx2.ndx
cat _ndx1.ndx _ndx2.ndx >_ndx.ndx
g_hbond -r 0.34 -f traj.trr -s production.tpr -n _ndx.ndx -num OW-HW-OW_hbnum.xvg
g_hbond -r 0.34 -f traj.trr -s production.tpr -n _ndx.ndx -num OW-HW-O_hbnum.xvg
rm -f _ndx1.ndx _ndx2.ndx _ndx.ndx
#####################################
g_select -s production.tpr -select "name OW, HW1, HW2" -on _ndx1.ndx
g_select -s production.tpr -select "name OP" -on _ndx2.ndx
cat _ndx1.ndx _ndx2.ndx >_ndx.ndx
g_hbond -r 0.354 -f traj.trr -s production.tpr -n _ndx.ndx -num Ow-Hw-Ow_hbnum.xvg
g_hbond -r 0.354 -f traj.trr -s production.tpr -n _ndx.ndx -num Ow-Hw-O_hbnum.xvg
###############################################
gmx select -s production.tpr -select "name OW, HW1, HW2" -on _ndx1.ndx
gmx select -s production.tpr -select "name OP" -on _ndx2.ndx
cat _ndx1.ndx _ndx2.ndx >_ndx.ndx
gmx hbond -r 0.354 -f traj.trr -s production.tpr -n _ndx.ndx -num Ow-Hw-
Ow_hbnum.xvg
gmx hbond -r 0.354 -f traj.trr -s production.tpr -n _ndx.ndx -num Om-Hm-O_hbnum.xvg
######################
g_select -s production.tpr -select "name O, H" -on _ndx1.ndx
g_hbond -r 0.35 -f traj.trr -s production.tpr -n _ndx1.ndx -num Om-Hm-O_hbnum.xvg
###################################################################################
############
Autocorrelation functions run:
To generate trajectories for analysis of vac and dipolesac we need higher frequency
of output of coordinates and velocities!
Step 1: Compile run1:
grompp -f run1.mdp -po prodrun.mdp -c ../prodnvt/production.tpr -o production.tpr -
t ../prodnvt/state.cpt -p ../prodnvt/processed.top
#########################
or:::::::
grompp -f run1.mdp -po prodrun.mdp -c production.tpr -o production.tpr -t state.cpt
-p processed.top
Step 2: run:
mdrun -s production.tpr -v -c final.gro
Calculation of vac and spectra:
g_velacc -f traj.trr -s production.tpr -n index.ndx -o vacO -os specO
