[gmx-users] mdrun failure plus other questions

[Chris O'Brien]

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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