Questions About CHARMM36 Parameters for DNA Systems

User discussions
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1

@jalemkul
GROMACS version:2023.3
Hello,
I have some questions about parameters for CHARMM36 in DNA systems:

1**) Fourierspacing Value:**
I read that the Fourierspacing value should generally be [cutoff value]/8. For CHARMM36, this would mean a value of 0.15. However, the GROMACS tutorial mentions using 0.16. Does this difference have a significant impact?

2)rlist Value:
Regarding the rlist parameter for CHARMM36, the GROMACS manual here mentions rlist=1, while the latest tutorials suggest using 1.4.

I plan to use the following parameters:
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
vdwtype = cutoff
vdw-modifier = force-switch
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rvdw-switch = 1.0 ; short-range van der Waals cutoff (in nm)
rvdw = 1.2
rlist = 1.2 ;gromacs
dispcorr = no
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT

Could you please confirm if these settings are correct or suggest adjustments?

Thank you in advance for your help!

2

I’ve never investigated it. I doubt the difference would be large.

The manual mentions a default value; there is no reason to think that value is physically meaningful or appropriate. The value for CHARMM is 1.4, although of course this gets tuned by the Verlet algorithm.

3

hello,
thank you so much