[gmx-users] au--protein separate equilibration

[fatemeh ramezani]

1. For separate equilibration of AU and Protein, I'm using this em.mdp file for equilibration in step 1, that Protein and SOL are frozen:
title               =  n.pdb
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
dt                  =  0.002
nsteps              =  40000
;constraint_algorithm  = shake
;shake_tol           = 0.0001
;nstenergy           =  10
;nstxtcout           =  10
;nstlist             =  5
ns_type             =  grid
rlist               =  1
coulombtype         =  PME
rcoulomb            =  1
rvdw                =  1.2
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes
;       Energy minimizing stuff
emtol               =  1000.0
emstep              =  0.01
freezegrps          =  Protein   SOL
freezedim           =  Y Y Y    Y Y Y  
comm_mode           =  None

2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain:
title               =  n.pdb
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
dt                  =  0.002
nsteps              =  40000
;constraint_algorithm  = shake
;shake_tol           = 0.0001
;nstenergy           =  10
;nstxtcout           =  10
;nstlist             =  5
ns_type             =  grid
rlist               =  1
coulombtype         =  PME
rcoulomb            =  1
rvdw                =  1.2
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes
;       Energy minimizing stuff
emtol               =  1000.0
emstep              =  0.01
freezegrps          =    AU   AUI     AUC   
freezedim           =  Y Y Y  Y Y Y  Y Y Y 
comm_mode           =  None

 

3. In simulation, I'm using this md.mdp file:
title                    = Yo
cpp                      = /lib/cpp
define                   = 
integrator               = md    
tinit                    = 0.00000
dt                       = 0.002
nsteps                   = 250000
nstxout                  = 2500
nstvout                  = 2500
nstlog                   = 500
nstenergy                = 250
nstxtcout                = 0
pbc                      = xyz  
rlist                    = 1.00
coulombtype              = PME             
r_coulomb                = 1.00
fourierspacing           = 0.10
pme_order                = 6
ewald_rtol               = 1e-6
vdw-type                 = switch                   
rvdw-switch              = 0.90
rvdw                     = 1.00
tcoupl                   = nose-hoover
tc_grps                  = SOL AUS AUB AUI
tau_t                    = 0.1 0.1 0.1 0.1
ref_t                    = 300 300 300 300
Pcoupl                   = no             
gen_vel                  = yes
gen_temp                 = 10 
gen_seed                 = 173529
; GolP has been tested with lincs only
constraints              = none
constraint_algorithm     = lincs
lincs_order              = 4
lincs_iter               = 1
lincs_warnangle          = 80
freezegrps               = AU AUI
freezedim                = Y Y Y Y Y Y 
comm_mode                 = None
Are these .mdp file right?

Fatemeh Ramezani