normal The switch/shift interaction settings

  • imankatouzian
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1 month 2 weeks ago #8432 by imankatouzian
The switch/shift interaction settings was created by imankatouzian
Hello,

I have just produced my minimization-vacuum.tpr file successfully, however, I get this note and I do not know how to fix it can sb help me with this?

NOTE : The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! Below is the input of my minimization-vacuum.mdp file : integrator = steep dt = 0.02 nsteps = 10 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout = 100 xtc-precision = 10 rlist = 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = no tc-grps = Protein tau-t = 1.0 ref-t = 300 cutoff-scheme = group thanks[file minimization-vaccum.mdp]:
The switch/shift interaction settings are just for compatibility; you
will get better performance from applying potential modifiers to your
interactions!

Below is the input of my minimization-vacuum.mdp file :

integrator = steep
dt = 0.02
nsteps = 10
nstxout = 0
nstvout = 0
nstlog = 100
nstxtcout = 100
xtc-precision = 10
rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
tcoupl = no
tc-grps = Protein
tau-t = 1.0
ref-t = 300
cutoff-scheme = group


thanks

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  • peterkroon
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1 month 2 weeks ago #8433 by peterkroon
Replied by peterkroon on topic The switch/shift interaction settings
From cgmartini.nl/images/parameters/exampleMDP/martini_v2.x_new.mdp :

cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

coulombtype = cutoff
coulomb-modifier = Potential-shift-verlet
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1


You'll need to add the options relevant to you, such the integrator etc.

HTH
Peter

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