[gmx-users] mdrun failure plus other questions

[Itamar Kass]

   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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040224/d8a83654/attachment.html>