[gmx-users] why protein comes out of the box

sangeeta kundu sangeeta0983 at yahoo.co.in
Wed Feb 7 12:48:32 CET 2007

Dear Sir,
      I am facing one  problem, I gave the MD run of a protein of approximately 70 residues for 10ns, after 1 ns run part of protein was getting out of the waterbox and at the end of 10 ns I found that almost half of the protein was coming out of the waterbox, I gave the simulation under NPT condition at 46C and 1BAR pressure, I used  43a1 force field and spc water.
  This is my md.mdp file
   title               =  Yo
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000000  ; total 10 ns.
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.12
pme_order           =  4
ewald_rtol          =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein  SOL
tau_t               =  0.1      0.1
ref_t               =  319      319
; Energy monitoring
energygrps          =  Protein  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  319.0
gen_seed            =  173529

  I used the 43a1 force field, and prepared the water box by the commands 
  editconf -bt triclinic -f conf.pdb -o box.pdb -c -d 1.0 
  genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top
  But I wonder that  while executing the command 
  grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr 
  it did not display any charge , so I did not add any counterion to my protein, in the subsequent steps em.pdb and pr.mdp files were produced and in both the cases the protein was almost in  the centre of the box, while I took the snapshot after 1ns the protein was still at the centre , but after 1 ns it was coming to one corner of the box, and finally almost half of it was outside the box when I completed the run, I can not detect why it is coming outside the box?
  Where am I doing mistake? Another question is how can I understand that the simulation has been completed successfully?
  Please help.

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