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

[Arik Cohen]

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.
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"); 
 

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