[gmx-users] mdrun producing 0 steps, 0 ps

[Travis Craddock]

Hello,

I'm trying to perform an energy minimization on a Tubulin-GTP-GDP complex in 
a water solvent with sodium ions.  I use the following command to setup up 
the minimization,

> grompp -f em.mdp -c tubulin_b4em.gro -p tubulin3.top -o tubulin_em.tpr

My energy minimization file em*.mdp is:

title               = Tubulin 
cpp                 = cpp ; location of cpp  
define              = -DFLEX_SPC ; Use Ferguson's Flexible water 
model [4] 
constraints         = none 
integrator          = steep 
dt                  = 0.002    ; ps ! 
nsteps              = 500 
nstlist             = 10  
ns_type             = grid 
rlist               = 0.9 
coulombtype         = PME ; Use particle-mesh ewald  
rcoulomb            = 0.9 
rvdw                = 1.0 
fourierspacing      = 0.12 
fourier_nx          = 0 
fourier_ny          = 0 
fourier_nz          = 0 
pme_order           = 4 
ewald_rtol          = 1e-5
optimize_fft        = yes 
; 
;       Energy minimizing stuff 
; 
emtol               = 1000.0 
emstep              = 0.01 

When I try and run the energy minimization with the following command,

> mdrun -s tubulin_em.tpr -o tubulin_em.trr -c tubulin_b4pr.gro -g em.log -e 
em.edr 

I get the following output (after the initial option list),



Back Off! I just backed up em.log to ./#em.log.2#
Reading file tubulin_em.tpr, VERSION 3.3.2 (single precision)

Back Off! I just backed up em.edr to ./#em.edr.2#
starting mdrun 'TUBULIN ALPHA CHAIN'
0 steps,      0.0 ps.


Back Off! I just backed up tubulin_e,.trr to ./#tubulin_e,.trr.1#
Writing final coordinates.

Back Off! I just backed up tubulin_b4pr.gro to ./#tubulin_b4pr.gro.2#



    M E G A - F L O P S   A C C O U N T I N G

   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=Tabulated        W3=SPC/TIP3p    W4=TIP4p (single or pairs)
   NF=No Forces

 Computing:                        M-Number         M-Flops  % of Flops
-----------------------------------------------------------------------
 LJ                                0.444057       14.653881     1.9
 Coulomb                           0.442386       11.944422     1.5
 Coulomb [W3]                      0.031861        2.548880     0.3
 Coulomb + LJ                      0.326092       12.391496     1.6
 Coulomb + LJ [W3]                 0.087734        7.983794     1.0
 Coulomb + LJ [W3-W3]              2.154199      527.778755    67.2
 Outer nonbonded loop              0.234492        2.344920     0.3
 1,4 nonbonded interactions        0.015595        1.403550     0.2
 NS-Pairs                          6.889484      144.679164    18.4
 Reset In Box                      0.106652        0.959868     0.1
 Shift-X                           0.426456        2.558736     0.3
 CG-CoM                            0.037769        1.095301     0.1
 Bonds                             0.008622        0.370746     0.0
 Angles                            0.012568        2.048584     0.3
 Propers                           0.004533        1.038057     0.1
 Impropers                         0.004403        0.915824     0.1
 Virial                            0.106679        1.920222     0.2
 Update                            0.106652        3.306212     0.4
 Calc-Ekin                         0.213304        5.759208     0.7
 Constraint-V                      0.106652        0.639912     0.1
 Constraint-Vir                    0.294435        7.066440     0.9
 Settle                            0.098145       31.700835     4.0
-----------------------------------------------------------------------
 Total                                           785.108807   100.0
-----------------------------------------------------------------------

               NODE (s)   Real (s)      (%)
       Time:      1.130      1.000    113.0




When I perform my subsequent position restraint, and MD runs there is no 
simulation to observe.  Am I missing something?  Any help would be 
appreciated.  Thanks.

Travis Craddock
Department of Physics         
University of Alberta