Regarding Hydrogen bonding

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1

Hi All,
Thanks for all the suggestions made by you. I am using ch2lmp tool to import data from PDB and PSF. I want to include the effect of hydrogen bonding in the imported molecule. Please suggest how can I add it in my input script?

Here is the input script which I have got from ch2lmp tool.

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/long 8 10
pair_modify mix arithmetic
kspace_style pppm 1e-4

read_data ubqp_autopsf.data

special_bonds charmm
fix 1 all nve
fix 2 all shake 1e-6 500 0 m 1.0
velocity all create 0.0 12345678 dist uniform

thermo 1
thermo_style multi
timestep 0.5

restart 10 ubqp_autopsf.restart1 ubqp_autopsf.restart2
dump 1 all atom 10 ubqp_autopsf.dump
dump_modify 1 image yes scale yes

run 20

2

Hi All,
            Thanks for all the suggestions made by you. I am using ch2lmp
tool to import data from PDB and PSF. I want to include the effect of
hydrogen bonding in the imported molecule. Please suggest how can I add it
in my input script?

huh??

hydrogen bonding is a "side effect" of the force
field that you are using there is nothing to add.

please have a look at the papers describing the
force field that you are using.

axel.