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标题: 求助：mdrun之后报错 [打印本页]

作者
Author: geralt14 时间: 2021-10-19 14:43
标题: 求助：mdrun之后报错
纯新手小白求助！
(, 下载次数 Times of downloads: 17)
报错内容。mdrun的指令是gmx mdrun -nt 4 -pin on -pme gpu -nb gpu -bonded gpu -update gpu -v -deffnm md
md.mdp:
title          = OPLS Lysozyme MD simulation
; Run parameters
integrator          = md             ; leap-frog integrator
nsteps          = 50000000             ; 2 * 50000000 = 100000 ps (100 ns)
dt                   = 0.002             ; 2 fs
; Output control
nstxout          = 25000             ; save coordinates every 50.0 ps
nstvout          = 25000             ; save velocities every 50.0 ps
nstenergy          = 25000             ; save energies every 50.0 ps
nstlog          = 25000             ; update log file every 50.0 ps
nstxout-compressed    = 25000                   ; save compressed coordinates every 50.0 ps
                                                ; nstxout-compressed replaces nstxtcout
compressed-x-grps    = System                   ; replaces xtc-grps
; Bond parameters
continuation          = yes             ; Restarting after NPT
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
cutoff-scheme          = Verlet
ns_type          = grid             ; search neighboring grid cells
nstlist          = 10                      ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb          = 1.0             ; short-range electrostatic cutoff (in nm)
rvdw          = 1.0             ; 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 is on
tcoupl          = V-rescale             ; modified Berendsen thermostat
tc-grps          = Protein_LTSV  water_and_ions       ; two coupling groups - more accurate
tau_t          = 0.1       0.1       ; time constant, in ps
ref_t          = 310       310       ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman       ; Pressure coupling on in 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             ; Velocity generation is off

作者
Author: sobereva 时间: 2021-10-20 03:13
绝对不要用constraints = all-bonds ，论坛里我都说了N次了（PS：网上一些以讹传讹的教程太害人了）

(, 下载次数 Times of downloads: 20)

如果改成真正该用的constraints = hbonds之后还这样，去掉-update gpu再试

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