[gmx-users] A problem with a "detaching Calpha/s"

[Mark Abraham]

Arik Cohen wrote:
> Dear GROMACS users,
> 
> While running a simple MD simulation with both a small protein such as 
> BPTI and a larger one such as tmRBP_Unliganded_2FN9.pdb, I'm 
> encountering an odd situation in which one (in the case of BPTI) or 
> several Calphas (in the later case) are "detaching them selfs" from the 
> main group.

"main group" of what? Do the atoms bound to them move also? Are you 
seeing a periodicity artefact?

Mark

> The problem appeared only after adding salt to the simulation(at least 
> in the case of BPTI).
> I would appreciate any suggestions and comments on the matter.
> 
> Thanks
> 
> Arik
> 
> The run files are:
> 
> *em.mdp:*
>  
> title               =  tmRBP_Unliganded_2FN9 Minimization
> integrator          =  steep      ; (steep)using steepest descent
> nsteps              =  50000
> nstlist             =  1
> rlist               =  1.0
> coulombtype         =  PME
> rcoulomb            =  1.0
> vdw-type            =  cut-off
> rvdw                =  1.0
> nstenergy           =  10
> emtol               =  5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
> 
> 
> *pr.mdp
> *
> title               =  tmRBP_Unliganded_2FN9 PR
> integrator          =  md
> nsteps              =  50000
> dt                  =  0.002 ;(in ps) doing a 100ps traj.
> constraints         =  all-bonds
> nstlist             =  10 ; neighbour list updates every number of steps
> rlist               =  1.0
> coulombtype         =  PME
> rcoulomb            =  1.0
> vdw-type            =  cut-off
> rvdw                =  1.0
> tcoupl              =  Berendsen
> tc-grps             =  Protein non-protein
> tau-t               =  0.1 0.1
> ref-t               =  298 298
> Pcoupl              =  Berendsen
> tau-p               =  1.0
> compressibility     =  5e-5 5e-5 5e-5 0 0 0
> ref-p               =  1.0
> nstenergy           =  100
> define              =  -DPOSRES ; include posre.itp(position restraint) file
> 
> *run.md
> *title               =  tmRBP_Unliganded_2FN9
> integrator          =  md
> nsteps              =  300000
> dt                  =  0.001
> constraints         =  all-bonds
> nstlist             =  10
> rlist               =  1.0
> coulombtype         =  PME
> rcoulomb            =  1.0
> vdw-type            =  cut-off
> rvdw                =  1.0
> tcoupl              =  V-rescale  ;V-rescale
> tc-grps             =  Protein non-protein
> tau-t               =  0.8 0.8
> ref-t               =  298 298
> nstxout             =  1000
> nstvout             =  1000
> nstxtcout           =  1000
> nstenergy           =  1000
> 
> 
> 
> The runs commands are(integrated inside a C++ code):
> 
> SysCommand1 = "echo 6 | pdb2gmx -f " + FileName + " -water tip3p";
> 
>  system("editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro");
> 
> system("genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro");
> 
> 
> minimization:
> --------
>  if(Mode == "NoSalt")
>     {
>      system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o em.tpr");
>  
>      //system("mpirun -np 4 mdrun -v -deffnm em");
>     }
>   if(Mode == "WithSalt")
>     {
>       system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o em.tpr");
>      
>       system("mpirun -np 4 mdrun -v -deffnm em");
>     }
> 
> 
> Salting:
> --------
>  system("echo 12 | genion -s em.tpr -conc 0.1 -neutral -o solvated.gro");
>  
> pr:
> ----
> system("grompp -f MDP/prmd.mdp -p topol.top -c em.gro -o pr.tpr");
>   /* The actual run*/
>   system("mpirun -np 4 mdrun -v -deffnm pr"); 
>  
>