[gmx-users] mdrun failure plus other questions

Itamar Kass ikass at cc.huji.ac.il
Tue Feb 24 18:04:01 CET 2004

   Regarding the crash when doing MD after EM, try to look at the output log, you will see the number of the atom which probably make problems e.g. atom #200 at:
Step=  533, Dmax= 2.5e-03 nm, Epot= -3.51631e+05 Fmax= 2.02906e+03, atom= 200
try to look at it using VMD or SpdbViewer etc.
Regarding the question about grouping the residues, you can use make_ndx to index the three residue into one group.
About the different chains, try to put letters as index instead of using MODEL-TER-ENDMDL, it should work.

  ----- Original Message ----- 
  From: Chris O'Brien 
  To: gmx-users at gromacs.org 
  Sent: Tuesday, February 24, 2004 5:29 PM
  Subject: [gmx-users] mdrun failure plus other questions

  Dear gmx-users,

  I am having trouble getting an mdrun to start successfully.  My system is a periodic box containing 20 polylactide 50-mers of the residue form SL1-(SL2)n-SL3.  Prior to an mdrun, I minimized the system with cg to Epot = -5.1736e4 and Fmax = 0.979.  My grompp command line for the input to the mdrun includes the *.gro and the *.trr file from the output of the final minimization.  However, when I try an mdrun, the system behaves as if there are very large forces present: I get LJ (SR) values of 1e10, "1-4 interactions at a distance greater than 1" warnings to screen and "1-4 interaction not within cutoff" in the -debug file, the temperature and pressure increase to the order of 1e18, and everything goes "nan".  Also, it says "Large VCM (group rest): -0.0000,   -0.0000,  -0.0000.  How is (negative) zero large?

  I have tried changing several parameters to see if it would help, to no avail.  Here is a representative mdp file for the simulations after I had turned off the T and P coupling.

  define                   = 
  integrator               = md
  dt                       = 0.0005 ;ps
  nsteps                   = 10000 ; 
  nstcomm              = +1
  nstxout                  = 5000
  nstvout                  = 5000
  nstlog                   = 5000
  nstenergy                = 5000
  nstfout               = 5000
  nstxtcout                = 5000
  ;xtc_grps                 = SL1 SL2     SL3
  energygrps               = SL1  SL2     SL3
  nstlist                  = 5
  ns_type                  = grid
  pbc                           = xyz
  rlist                    = 1.0
  coulombtype              = cut-off
  rcoulomb                 = 1.0
  vdwtype              = cut-off
  rvdw                     = 1.0
  tcoupl                   = no;berendsen
  tc-grps                  = SL1  SL2     SL3
  tau_t                    = 0.1 0.1 0.1
  ref_t                    = 300 300 300
  Pcoupl                   = no;berendsen
  pcoupltype                    = isotropic 
  tau_p                    = 2.0
  compressibility          = 4.5e-5
  ref_p                    = 1.0
  gen_vel                  = yes
  gen_temp                 = 50
  gen_seed                 = 173529
  constraints              = none

  The box is a 20 nm cube, so the molecules aren't seeing their duplicates.  

  A few somewhat related topics that this question brought to mind:

  1. I don't think I really need to couple or record separately for each residue.  How do I declare this in the mdp?  With "system", "Protein", or something else?

  2. Although the pdb file used to make the system includes 20 distinct polymer chains, the *.top file lists only a single molecule (Protein).  Is this problematic?  Pdb2gmx wouldn't run if I didn't remove the MODEL-TER-ENDMDL lines from the pdb file.  With smaller systems, I can work around this with chain identifiers, but that doesn't work so well when the size and number of polymers gets large, and I would rather have a single *.top file than multiple *.itp files.

  My apologies for the jumble of questions, and I look forward to any input people might have.

  Thank you,

  Chris O'Brien

  Department of Chemical Engineering
  Clemson University
  Clemson, SC  29634-0909

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