From: Hossein Geraili <geraili.hsn.gmail.com>
Date: Thu, 5 Oct 2017 13:14:50 +0330

Dear Amber users,
I am not using the Amber software, but I could not find a place that people
would know about the right combination of Amber and MD. Please if you can
comment help me with this. I am using Lammps for my simulation.

All the bonded energy (bond, dihedral, improper) are equal to article's
value, but the angle energy value is so big(1134 kJ/mol but 53 kJ/mol in
the article). What can be wrong? I checked the angle parameters several
times as well as the commands, but none of my theoretical friends found out
what is wrong. If other energies were wrong too, it would not be a problem.
Also, I checked the angle parameters from other sources( Amber force field
article for my molecule) and they are almost the same. Moreover, before
this Amber ff, I used Charmm force field and I did not get right values for
density, and recently I checked it and saw its angle energy is also so big.
Because of these big angle energy values total and potential energy in
both( Charmm and Amber) simulations are big positive values, but in both
articles, they are negative. Is there something special about angle
charmm and amber force field?

I am using Amber force field. Maybe this will not be helpful, but this is
my input in case that somebody can use these to figure out the problem:

units real
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style cvff
pair_style lj/charmm/coul/long 13 15
pair_modify mix arithmetic tail yes
kspace_style ewald 1.0e-4
read_data ionicdata.data
neighbor 2.0 bin
neigh_modify delay 2 every 1 check yes
special_bonds amber

minimize 1.0e-10 1.0e-12 10000 10000
velocity all create 313 4928459 rot yes dist gaussian
timestep 2.0

run_style respa 4 2 2 2 pair 1 kspace 4

fix 1 all nve
run 10000
unfix 1
fix 3 all npt temp 313 313 30.0 iso 0.9671848 0.9671848 700.00
run 3000000

Please if you have any comment, let me know.
Thanks in advance

Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
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Received on Thu Oct 05 2017 - 03:00:03 PDT
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