[gmx-users] re octane box help/probelms

[Chris Shaw]

Hi Dallas 

Thanks for getting back to me, here is my .mdp file

;

; octane run

;

title = Yo

cpp = /lib/cpp

;Run Parameters

integrator = md

dt = 0.002 ; ps !

nsteps = 25000 ; total 50 ps.

nstcomm = 1

nstxout = 250

nstvout = 1000

nstfout = 0

nstlog = 100

nstenergy = 100

nstlist = 10

ns_type = grid

pbc = xyz

;Bonds

constraints = lincs

lincs_order = 4

;vdw

vdw_type = cut-off

rlist = 1.0

rvdw = 1.0

;Electrostatics 

coulombtype = pme

fourierspacing = 0.12

pme_order = 4

ewald_rtol = 1e-5

rcoulomb = 1.0

; Berendsen temperature coupling is on in one group

Tcoupl = berendsen

tc-grps = C8 

tau_t = 0.1

ref_t = 300 

; Energy monitoring

energygrps = C8 

; isotropic pressure coupling is now on

Pcoupl = berendsen

Pcoupltype = isotropic

tau_p = 1 

compressibility = 4.5e-5 

ref_p = 1.0 

; Generate velocites is off at 300 K.

gen_vel = yes

gen_temp = 300.0

gen_seed = 173529

dispcorr = EnerPres 

 

Is this right?. Also could you check the way I have done PME and vdv cutoff is this right as well (for future simulations)

Cheers for the help

Chris :-)




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