[gmx-users] Exploding Protein with 4.6 and 4.5.5

[XAvier Periole]

Try to use constrains = all-bonds which is the way to use Gromos force fields. 

On Mar 26, 2012, at 12:30, SebastianWaltz <sebastian.waltz at physik.uni-freiburg.de> wrote:

> Dear Gromacs user,
> 
> I try to simulate the human Villin head peace HP35 in approx. 6000 water
> molecules (spc) with the gromos ff ffG53a6. Using the 4.0.7 version the
> NPT equilibration for 5ns with position restraint protein (lincs) atoms
> and a integration step of 0.002 using the leap-frog integrator works
> just fine. Switching to the 4.5.5 or the 4.6 version with heterogeneous
> acceleration is leading to an exploding protein after a few ps. Changing
> the integration time step to 0.0002 delays the explosion for few ps but
> does not avoid it. The parameters in mdp file for the 4.6 version are
> the following:
> 
> ;
> title                    = ttt
> cpp                     =  /lib/cpp
> include               = -I../top
> constraints         = hbonds
> integrator           =  md
> cutoff-scheme    =  verlet
> 
> define                 =  -DPOSRES                      
> ;constraint_algorithm = shake
> dt                        =  0.0002                
> nsteps                 =  2500000               
> nstcomm            =  10                   
> nstxout               =  1000                  
> nstvout               =  1000                   
> nstfout                =  1000                    
> nstlog                 =  1000                  
> nstenergy           =  5000                  
> nstxtcout             =  10
> 
> xtc_grps            =  Protein
> 
> nstlist                =  25                     
> ns_type             =  grid                    
> rlist                   =  1.2                    
> 
> coulombtype      =  PME                  
> rcoulomb            =  1.2                    
> vdwtype              =  cut-off
> rvdw                   =  1.2                   
> fourierspacing    =  0.12                  
> pme_order         =  6                     
> optimize_fft        =  yes
> pbc                     =  xyz
> Tcoupl                 =  v-rescale
> tc-grps                =  Protein Non-Protein
> tau_t                   =  0.1 0.1
> ref_t                    =  300 300
> 
> energygrps          =  Protein Non-Protein
> 
> Pcoupl                 =  berendsen
> tau_p                   =  0.5
> compressibility     =  4.5e-5
> ref_p                     =  1.0
> refcoord_scaling   =  all
> Pcoupltype            =  isotropic
> gen_vel                 =  yes
> gen_temp             =  300
> gen_seed              =  -1
> 
> 
> Any help is very welcomed.
> 
> Dears sincerely,
> 
> Sebastian
> -- 
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