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

[Tsjerk Wassenaar]

Hi Travis,

It looks like grompp doesn't parse your .mdp file properly. You should
get an mdout.mdp which contains the parameters as they ended up in
your .tpr file. Check these against your .mdp file. Alternatively you
can 'gmxdump' your .tpr file to check the parameters. Was the .mdp
file originating from a windows machine and are you now under linux
(vv)? Then dos2unix will probably do the trick.

Hope it helps,

Tsjerk

On Tue, Jul 1, 2008 at 12:26 AM, Travis Craddock
<tcraddoc at phys.ualberta.ca> wrote:
> 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
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623