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标题: 使用GBSA隐式溶剂模型模拟时mdp如何设置 [打印本页]

作者
Author: 苏玖染 时间: 2019-12-16 17:03
标题: 使用GBSA隐式溶剂模型模拟时mdp如何设置
如题，我设置了一些mdp参数，但是跑em总是出现力过大的问题

integrator          = steep
nsteps                = 5000
emtol                = 1000
emstep                = 0.01
comm_mode       = angular
nstcomm             = 10

nstxout             = 250       ; save coordinates to .trr every 250 steps
nstvout             = 0       ; don't save velocities to .trr
nstfout             = 0       ; don't save forces to .trr

nstxout-compressed    = 500       ; xtc compressed trajectory output every 500 steps
compressed-x-precision = 1000
nstlog                = 500       ; update log file every 500 steps
nstenergy             = 500       ; save energies every 500 steps
nstcalcenergy       = 100

cutoff-scheme    =  group
rlist             =  60
rvdw             =  60
rcoulomb       =  60
coulombtype       =  cut-off
vdwtype          =  cut-off
bd_fric          =  0
ld_seed          =  -1
pbc                =  no
ns_type          =  simple
constraints       = h-bonds
lincs_order       = 4
lincs_iter       = 1
lincs-warnangle    = 30

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm          = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii             = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                = 5
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent    = 80
; Salt concentration in M for Generalized Born models
gb_saltconc             = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha          = 1
gb_obc_beta             = 0.8
gb_obc_gamma          = 4.85
gb_dielectric_offset    = 0.009
sa_algorithm          = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension    = -1

请问有哪里有问题，因为我的蛋白是自己建立的，做成之后是直线型的，需要通过隐式溶剂下预优化来使之平衡，但一直出错，跑em一直出现力过大，降不下来的问题，但从实际看，不应该存在这样的问题，也就是说我的分子没有明显不合理的接触，去掉隐式溶剂模型的相关设置之后跑真空的，却可以跑

作者
Author: sobereva 时间: 2019-12-16 17:46
参考例子
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跑一般蛋白没问题

作者
Author: 苏玖染 时间: 2019-12-16 18:27

sobereva 发表于 2019-12-16 17:46
参考例子

谢谢sob老师

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