[gmx-users] Shell MD

[yiran870804]

Dear sir：
 
Thank you for reading my letter. 
I have a few problems  in Shell MD

 ....      . I do not know how to set the parameter in the*.mdp file of shell md.So I hope to obtain your help.
 And this is my own *.mdp file below

 
include                  =
define                   = 
integrator               = sd
tinit                    = 0
dt                       = 0.004
nsteps                   =  10000000
simulation_part          = 1
init_step                = 0
comm-mode             nstcomm       = Linear
              = 100
comm-grps                = System 
bd-fric                  = 1
ld-seed                  = 1993 
emtol                    = 10
emstep                   = 0.01
niter                    = 20
fcstep                   = 0
nstcgsteep               = 1000
nbfgscorr                = 10 
rtpi                     = 0.05 
nstxout                  = 1000000
nstvout                  = 1000000
nstfout                  = 1000000
nstlog                   = 10
nstenergy                = 10
nstxtcout                = 10
xtc_precision            = 10
xtc-grps                 =
energygrps               = CR1 
nstlist                  = 1
ns_type                  = grid
pbc                      = xyz
periodic_molecules       = no  
rlist                    = 2.0 
coulombtype              = User
rcoulomb_switch          = 0.0
rcoulomb                 = 2.0
epsilon_r                = 1
epsilon_rf               = 1
vdw_type                 = User
rvdw_switch              = 0.0
rvdw                     = 2.0
DispCorr                 = No
table_extension          = 0
energygrp_table          = CR1 CR1
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = yes 
implicit_solvent         = No 
gb_algorithm             = Still
nstgbradii               = 1
rgbradii                 = 2
gb_epsilon_solvent       = 80
gb_saltconc              = 0
gb_obc_alpha             = 1
gb_obc_beta              = 0.8
gb_obc_gamma             = 4.85
sa_surface_tension       = 2.092 
tcoupl                   = berendsen
tc-grps                  = System
tau_t                    = 0.3
ref_t                    = 800
Pcoupl                   = no
Pcoupltype               = isotropic
tau_p                    = 1
compressibility          = 6.5e-5
ref_p                    = 5.0
refcoord_scaling         = No
andersen_seed            = 815131 
QMMM                     = no
QMMM-grps                =        
QMmethod                 =      
QMMMscheme               = normal
QMbasis                  =        
QMcharge                 =   
QMmult                   =  
SH                       =   
CASorbitals              =
CASelectrons             =
SAon                     =
SAoff                    =
SAsteps                  =
MMChargeScaleFactor      = 1
bOPT                     =
bTS                      = 
annealing                =
annealing_npoints        =
annealing_time           =
annealing_temp           = 
gen_vel                  = yes
gen_temp                 = 313
gen-seed                 = 173529 
constraints              = none
constraint_algorithm     = Lincs
continuation             = no
Shake-SOR                = no
shake-tol                = 1e-04
lincs_order              = 4
lincs-iter               = 1
lincs_warnangle          = 30
morse                    = no 
energygrp_excl           = 
nwall                    = 0
wall_type                = 9-3
wall_r_linpot            = -1
wall_atomtype            =
wall_density             =
wall_ewald_zfac          = 3 
pull                     = no 
disre                    = No
disre-weighting          = Conservative
disre-mixed              = no
disre-fc                 = 1000
disre-tau                = 0
nstdisreout              = 100
orire                    = no
orire-fc                 = 0
orire-tau                = 0
orire-fitgrp             =
nstorireout              = 100
dihre                    = no
dihre-fc                 = 1000 
free-energy              = no
init-lambda              = 0
delta-lambda             = 0
sc-alpha                 = 0
sc-power                 = 0
sc-sigma                 = 0.3
couple-moltype           =
couple-lambda0           = vdw-q
couple-lambda1           = vdw-q
couple-intramol          = no 
acc-grps                 =
accelerate               =
freezegrps               =
freezedim                =
cos-acceleration         = 0
deform                   = 
E-x                      =
E-xt                     =
E-y                      =
E-yt                     =
E-z                      =
E-zt                     = 
user1-grps               =
user2-grps               =
userint1                 = 0
userint2                 = 0
userint3                 = 0
userint4                 = 0
userreal1                = 0
userreal2                = 0
userreal3                = 0
userreal4                = 0
 
Could you tell me which part of the parameter should be changed for Shell MD?
  
Your prompt attention to this letter would be highly appreciated.
 Thanks a lot.
 
                                                                                                                                                                                           Liyan
   
 
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