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zhuimeng08

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[交流] gromacs 用GPU版本跑动力学已有2人参与

gromacs 用GPU版本跑动力学能否给我传一份md.mdp文件！我这一直报错！很奇怪

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1楼 2014-04-22 15:32:15

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zhuimeng08

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2楼: Originally posted by 水儿CoCo at 2014-04-22 16:11:57
; Run parameters
integrator  = md       ; leap-frog integrator
nsteps    = 500000000 ; 2 * 500000000 = 1000000 ps (1000 ns)
dt       = 0.002    ; 2 fs
; Output control
nstxout    = 25 ...

谢谢！

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3楼2014-04-22 18:33:30

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水儿CoCo

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小木虫: 金币+0.5, 给个红包，谢谢回帖
月只蓝: 金币+5, 感谢分享。 2014-04-22 20:38:21

; Run parameters
integrator  = md       ; leap-frog integrator
nsteps    = 500000000 ; 2 * 500000000 = 1000000 ps (1000 ns)
dt       = 0.002    ; 2 fs
; Output control
nstxout    = 2500000       ;
nstvout    = 2500000       ;
nstenergy = 5000    ; save energies every 10 ps
nstlog    = 5000    ; update log file every 10 ps
nstxtcout = 5000    ; write .xtc trajectory every 10 ps
energygrps  = Protein_HEM  CLA

; Bond parameters
continuation = yes          ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints    = all-bonds    ; all bonds (even heavy atom-H bonds) constrained
lincs_iter    = 1          ; accuracy of LINCS
lincs_order    = 4          ; also related to accuracy
; Neighborsearching
ns_type    = grid    ; search neighboring grid cells
nstlist    = 5       ; 10 fs
rlist    = 0.9    ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9    ; short-range electrostatic cutoff (in nm)
rvdw       = 1.4    ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype    = PME    ; Particle Mesh Ewald for long-range electrostatics
pme_order    = 4       ; cubic interpolation
fourierspacing  = 0.16    ; grid spacing for FFT
; Temperature coupling
tcoupl    = V-rescale                   ; modified Berendsen thermostat
tc-grps    = Protein_HEM_CLA Water_and_ions ; two coupling groups - more accurate
tau_t    = 0.1 0.1                   ; time constant, in ps
ref_t    = 300 300                   ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl    = Parrinello-Rahman          ; pressure coupling is on for NPT
pcoupltype  = isotropic                   ; uniform scaling of box vectors
tau_p    = 2.0                         ; time constant, in ps
ref_p    = 1.0                         ; reference pressure, in bar
compressibility = 4.5e-5                   ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc       = xyz    ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel    = no       ; assign velocities from Maxwell distribution
有些参数自己修改吧