[gmx-users] Exploding Protein with 4.6 and 4.5.5

[SebastianWaltz]

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