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How to set Fourier spacing value?
- Cohan
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5 years 11 months ago #7664
by Cohan
How to set Fourier spacing value? was created by Cohan
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
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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- bart
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5 years 11 months ago #7665
by bart
Replied by bart on 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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- peterkroon
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5 years 11 months ago #7666
by peterkroon
Replied by peterkroon on topic How to set Fourier spacing value?
See also: gmx tunepme, which will do the hard work for you.
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- Cohan
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5 years 10 months ago #7674
by Cohan
Replied by Cohan on topic How to set Fourier spacing value?
thanks all
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