Force field comparison between CHARMM and AMBER99SB-ILDN

User discussions
1

Dear Gromacs users,

I am trying to perform a simulation for a protein-DNA system using GROMACS 2019. I would like to use both CHARMM22 and AMBER99SB-ILDN force fields. Actually, I want to compare both simulation results with our experimental observation and want to conclude that which force field is the best candidate for studying our system. Now, I have 200 ns simulation data using CHARMM force field. Please see the production input file below:

title = MD simulation
; Run parameters
integrator = md
nsteps = 200000000
dt = 0.002
; Output control
nstxout = 10000
nstvout = 10000
nstenergy = 10000
nstlog = 10000
nstxout-compressed = 10000
compressed-x-grps = System
continuation = yes
constraint_algorithm = lincs
constraints = h-bonds
lincs_iter = 1
lincs_order = 4
cutoff-scheme = Verlet
ns_type = grid
nstlist = 20
rlist = 1.2
coulombtype = pme
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
pme_order = 4
fourierspacing = 0.16
; Temperature coupling is on
tcoupl = Nose-Hoover
tc-grps = Protein_URA_CYT_ADE NA_CL_SOL
tau_t = 1.0 1.0
ref_t = 300 300

pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 5.0
ref_p = 1.0 ;
compressibility = 4.5e-5
refcoord_scaling = com
pbc = xyz
DispCorr = EnerPres
gen_vel = no

I used 1.2 nm simulation cut off using CHARMM. I saw, people were using 1.0 nm cut off using AMBER. Do I need to use same parameter file for force field comparison? I am confused regarding this issue.

Any kind of advice/ suggestions will be deeply appreciated.

Thanks in advance,
Snehasis Chatterjee

2

You should use the cutoffs prescribed by each force field. Nonbonded methods and settings should be treated as part of the force field itself and generally should not be changed. A force field comparison does not require identical nonbonded settings, it requires proper implementation of the force fields being examind.

3

Hi Prof. Lemkul,

Thank you very much for your valuable suggestion.

Snehasis

4

Dear Prof. @jalemkul ,

What will be the best and most commonly used force field for protein-DNA simulations?

Would Amber be good over Charmm?

Thank you!

5

The protein force fields are probably equally good, AMBER is probably somewhat better for dsDNA. You will need to get an AMBER force field port from some other source than what is provided with GROMACS; the currently distributed parameter sets are antiquated and not appropriate for modern simulations of nucleic acids.

6

Thank you very much Prof. Lemkul for your valuable advise!!