Fw: [gmx-users] au--protein separate equilibration

[fatemeh ramezani]

Dear Justin thanks for your reply and,
Please help me to correct the settings of .mdp files step by step .
By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that
I freeze AU atoms in it, minimization would be true?  


> 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 
> freezedim           =  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