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26.01.15

Run simulation with CTD terminal that was equilibrated on friday

  • create sim.mdp with following settings
integrator          =  md 
nsteps              =  2500000
tinit               =  0
dt                  =  0.004
comm_mode           =  linear
nstcomm             =  10 
nstcalcenergy       =  10
comm_grps           =  System
nstxout             =  0
nstvout             =  0
nstfout             =  0
nstlog              =  12500 
nstlist             =  20 
nstenergy           =  5000
nstxtcout           =  5000
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
fourierspacing      =  0.12
pme_order           =  4
ewald_rtol          =  1e-5
vdwtype             =  cut-off 
rvdw_switch         =  0
rvdw                =  0.95 
rlist               =  0.95
rcoulomb            =  0.95
DispCorr            =  no 
tc_grps             =  System
annealing           =  No
gen_vel             =  no 
continuation        =  no 
gen_seed            =  -1
constraints         =  all-bonds
constraint_algorithm=  lincs
lincs-iter          =  1
lincs-order         =  6
periodic_molecules  =  no
qmmm                =  no
tcoupl              =  v-rescale
tau_t               =  0.1
ref_t               =  298
ld_seed             =  -1
Pcoupl              =  Parrinello-Rahman
pcoupltype          =  isotropic
compressibility     =  4.5e-5
ref_p               =  1.0
tau_p               =  10.0
cutoff-scheme        = Verlet
verlet-buffer-drift  = 0.005
  • copy the sim.mdp to the the CTD folder
scp sim.mdp hvoehri@hvoehri.mpibpc.intern:~/230115_CTD/
  • grompp again
grompp -f sim.mdp -c ../eq/confout.part0001.gro -p ../init.top -o sim.tpr
  • Error message:

Program grompp, VERSION 4.6.6-dev-20140325-693d2e6-unknown
Source code file: /tmp/git-gromacs-4-6-department/src/kernel/calc_verletbuf.c, line: 231

Fatal error:
In molecule type 'Protein_chain_A' Virtual site 3fad construction involves atom 5, which is a virtual site of equal or high complexity. This is not supported.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Continue simulation of Villin

  • equilibration of the protein
grompp -f eq.mdp -p ../topol.top -c ../em.part0001.gro -o eq.tpr
  • leads to the following error
Program grompp, VERSION 4.6.6-dev-20140325-693d2e6-unknown
Source code file: /tmp/git-gromacs-4-6-department/src/kernel/readir.c, line: 2414

Fatal error:
52 atoms are not part of any of the T-Coupling groups
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
  • some atoms do not have a right assignment (???)
    • modify eq.mdp by exchanging the tcgroups from protein sol to Protein Non-Protein
vi eq.mdp
i # insert mode
ESC # command mode
:wq # save and quit
  • rerun grompp
grompp -f eq.mdp -p ../topol.top -c ../em.part0001.gro -o eq.tpr
  • connect to owl and run equilibration
ssh owl3
cd VILLIN/eq/
g_submit -s eq.tpr
  • setup the simulation, again error
grompp -f run.mdp -p ../topol.top -c ../eq/confout.part0001.gro -o sim.tpr 

Fatal error:
52 atoms are not part of any of the T-Coupling groups
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
  • rewrite run.mdp as previously
  • grompp the file, connect to owl3 and start simulation
grompp -f run.mdp -p ../topol.top -c ../eq/confout.part0001.gro -o sim.tpr 
ssh owl3
g_submit -s sim.tpr

Rerun Berendsen equilibration

  • Setup a new folder to completly start over
mkdir 260115_CTD
cp -r ../230115_CTD/charmm22star.ff/ ./
cp ../CTD.pdb ./
  • run pdb2gmx with interactive terminin selection
pdb2gmx -f CTD.pdb -vsite hydrogens -ter
  • create box, water and ions
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
editconf -f conf.gro -o box.gro -bt dodecahedron -d 1.5 -center 0 0 0
touch ions.mdp
grompp -f ions.mdp -p topol.top -c solvated.gro -o ions.tpr
genion -s ions.tpr -neutral -conc 0.15 -p topol.top -o ions.gro
  • this time do not create new folders for energy minimization etc., but run everything in the same folder
grompp -f em.mdp -p topol.top -c ions.gro -o em.tpr
mdrun -v -deffnm em
  • Run berendsen simulation
grompp -f berendsen.mdp -p topol.top -c em.part0001.gro -o berendsen.tpr
ssh owl3
g_submit berendsen.tpr

Lysozyme tutorial

  • Edit 1AKI.pdb by deleting all HOH lines in Vi
  • Create topology, restraint and post-processed structure file
pdb2gmx -f 1AKI-2.pdb -water spce
  • define box dimensions with editconf
    • -c to center the protein in the box
    • -d 1.0 to place the protein at least 1 nm from the box edge
editconf -f conf.gro -o box.gro -c -d 1.0 -bt cubic
  • Fill with solvent (water)
genbox -cp box.gro -cs spc216.gro -o solvated.gro -p topol.top
  • Generate ions
wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/Files/ions.mdp
grompp -f ions.mdp -c solvated.gro -p topol.top -o ions.tpr
genion -s ions.tpr -o solvated.gro -p topol.top -pname NA -nname CL -nn 8
  • Run Energy minimzation
grompp -f minim.mdp -c solvated.gro -p topol.top -o em.tpr
mdrun -v -deffnm em
  • Look at the Energy Minimzation
g_energy -f em.part0001.edr -o potential.xvg
xmgrace potential.xvg
  • Equilibration NVT
grompp -f nvt.mdp -c em.part0001.gro -p topol.top -o nvt.tpr
ssh owl3
g_submit -s nvt.tpr
  • Equilibration NPT
mkdir nvt # consider to rename the folder
cd nvt/
wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/Files/npt.mdp
grompp -f npt.mdp -c ../confout.part0001.gro -t ../state.cpt -p ../topol.top -o npt.tpr
ssh owl3
g_submit -s npt.tpr
  • run MD
mkdir md
cd md
wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/Files/md.mdp
grompp -f md.mdp -c ../nvt/confout.part0001.gro -t ../nvt/state.cpt -p ../topol.top -o md.tpr
ssh owl3
g_submit -s md.tpr