normal How to set Fourier spacing value?

  • Cohan
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5 months 5 days ago #7664 by Cohan
Cohan created the topic: How to set Fourier spacing value?
Hi all,
I am a simulating system consisted of peptides, polarizable waters, and CL- ions with a cubic box (20*20*20 nm^3). I decided to increase Fourier spacing value to speed up my run. How can I test the effect of Fourier spacing on my system to decide which value is suitable for me?

These are my mdp options:

integrator = md
dt = 0.03
nsteps = 10000
nstcomm = 100
comm-grps =
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxout-compressed = 0
compressed-x-precision = 100
compressed-x-grps =
energygrps =
cutoff-scheme = Verlet
nstlist = 30
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.01
coulombtype = PME
rcoulomb = 1.1
epsilon_r = 2.5
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
tcoupl = V-rescale
;nsttcouple = 1
;nstpcouple = 1
tc-grps = Protein non-Protein
tau_t = 1.0 1.0
ref_t = 300 300
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 18
compressibility = 3e-4
ref_p = 1.0
gen_vel = yes
continuation = no
gen_temp = 300
;gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
lincs_warnangle = 90
lincs-order = 4

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5 months 5 days ago #7665 by bart
bart replied the topic: How to set Fourier spacing value?
As far as I know that could change the balance of forces in your force field, thus you would have to show that your system still behaves the way it should. For example comparing the RDF of certain molecules to the original force field paper, but potentially much more tests would be needed. The effects of changing the balance of forces in a force field are hard to predict (the end is a weird mix of entropy and enthalpy). More info regarding the fourierspacing setting can be found in the gromacs manual.

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5 months 5 days ago #7666 by peterkroon
peterkroon replied the topic: How to set Fourier spacing value?
See also: gmx tunepme, which will do the hard work for you.

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4 months 4 weeks ago #7674 by Cohan
Cohan replied the topic: How to set Fourier spacing value?
thanks all

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