[gmx-users] Regarding minimization of POPE:POPG lipid bilayer

[naga raju]

  Dear gmx users,
                    I downloaded POPE.itp and lipid.itp files from Dr.Tieleman website http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies and POPG.itp file from Dr.Mikko Karttunen wesite http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml.
  I built a POPE:POPG bilayer in 3:1 ratio. When I am minimizing the bilayer, bonds in head groups are breaking in POPE and POPG lipid molecules.
   
  Here is my min.mdp input file
   
  cpp = /lib/cpp
  define = -DFLEXIBLE
  constraints = none
  integrator = steep
  nsteps = 2000
  ;
  ; Energy minimizing stuff
  ;
  emtol = 100
  emstep = 0.01
  nstcomm = 1
  ns_type = grid
  rlist = 1
  rcoulomb = 1.0
  rvdw = 1.0
  Tcoupl = no
  Pcoupl = no
  gen_vel = no
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  while creating *.tpr file using the above file for minimization, I am getting fallowing message.............
   
  
  calling /lib/cpp...
  In file included from pg-pe.top:5:
  dpopg.itp:10:8: warning: multi-line string literals are deprecated
  processing topology...
  Generated 344865 of the 344865 non-bonded parameter combinations
  Generating 1-4 interactions: fudge = 0.5
  Generated 344775 of the 344865 1-4 parameter combinations
  Excluding 3 bonded neighbours for POP 48
  Excluding 3 bonded neighbours for DPO 16
  Excluding 2 bonded neighbours for SOL 2481
  NOTE:
  System has non-zero total charge: -1.599999e+01
  
  processing coordinates...
  double-checking input for internal consistency...
  renumbering atomtypes...
  converting bonded parameters...
  # BONDS: 8242
  # ANGLES: 6257
  # PDIHS: 1712
  # RBDIHS: 1472
  # IDIHS: 272
  # LJ14: 1840
  initialising group options...
  processing index file...
  Making dummy/rest group for T-Coupling containing 10787 elements
  Making dummy/rest group for Acceleration containing 10787 elements
  Making dummy/rest group for Freeze containing 10787 elements
  Making dummy/rest group for Energy Mon. containing 10787 elements
  Making dummy/rest group for VCM containing 10787 elements
  Number of degrees of freedom in T-Coupling group rest is 32358.00
  Making dummy/rest group for User1 containing 10787 elements
  Making dummy/rest group for User2 containing 10787 elements
  Making dummy/rest group for XTC containing 10787 elements
  Making dummy/rest group for Or. Res. Fit containing 10787 elements
  Making dummy/rest group for QMMM containing 10787 elements
  T-Coupling has 1 element(s): rest
  Energy Mon. has 1 element(s): rest
  Acceleration has 1 element(s): rest
  Freeze has 1 element(s): rest
  User1 has 1 element(s): rest
  User2 has 1 element(s): rest
  VCM has 1 element(s): rest
  XTC has 1 element(s): rest
  Or. Res. Fit has 1 element(s): rest
  QMMM has 1 element(s): rest
  Checking consistency between energy and charge groups...
  writing run input file...
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  My question,
  Why bonds are breaking in POPG and POPE lipid molecules. 
  Any suggestion is appreciated.
                           Thank you in advance.
                                                                                         with regards,
                                                                                    Nagaraju Mulpuri.
   
   

 
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