Dear all,
I am learning to do MD of a simple unsolvated protein with LAMMPS. My results don't make sense. Here is
how I run it.
Starting starting from the 1HE9.pdb file from pdb.org, I deleted water from it, got he9p.pdb, and then generated
an he9.pgn file which is like:
package require psfgen
topology top_all22_prot.inp
pdbalias residue HIS HSE
pdbalias residue MSE MET
pdbalias atom MSE SE SD
pdbalias atom ILE CD1 CD
segment A {pdb he9p.pdb}
coordpdb he9p.pdb A
guesscoord
writepdb he9.pdb
writepsf he9.psf
exit
Using VMD to call the above file: vmd -e he9.pgn, I got 2 new files: he9.pdb and he9.psf.
Next I create yet another two new files needed by lammps: he9.in and he9.data by running this command:
perl charmm2lammps.pl all22_prot he9 -charmm -water=0
Now I got he9.in and he9.data. The input file he9.in is not exactly what I need, because at least I need an
implicit solvent model (pair_style is lj/charmm/coul/charmm/implicit ), so I changed it to:
units real
neigh_modify delay 2 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/charmm/implicit 9 10
pair_modify mix arithmetic
read_data he9.data
special_bonds charmm
fix 1 all nve
fix 2 all langevin 295 295 50 12345678
fix 3 all shake 1e-6 500 0 m 1.0 a 142
thermo 1
thermo_style multi
timestep 0.5
restart 49 he9.restart1 he9.restart2
dump 1 all atom 1 he9.dump
dump_modify 1 image yes scale no
run 100
Still the above file wouldn't give me the correct configuration, which is expected to be close to the initial native
state. I also tried to modify it with no luck. Does anybody have the knowledge about how to do it? Thank you do
much for your attention.
Xiuping Tao