[gmx-users] mdrun no structural output

[Justin A. Lemkul]

On 7/3/12 5:40 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I wanted to do a minimization with mdrun but the only output I get is:
> 3m71_minim.edr
> 3m71_minim.log
> 3m71_minim.trr
> But no structure file like .pdb i.e.
>
> There was no error in the step before where I prepared the input file with
> grompp. My .mdp file looks like this:
>
> define                  = -DPOSRES
> integrator              = steep
> emtol           = 10
> nsteps          = 5000
> nstenergy               = 1
> energygrps              = System
> coulombtype             = PME
> rcoulomb                = 0.9
> rvdw                    = 0.9
> rlist           = 0.9
> fourierspacing  = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
> pbc                     = xyz
>
>
>
> And also in this step there was no error.
> The end of the 3m71_minim.log looks like this:
>
>             Step           Time         Lambda
>             2647     2647.00000        0.00000
>
>     Energies (kJ/mol)
>             Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
>      5.35530e+02    2.26340e+03    1.17875e+04    1.31106e+02    4.73257e+03
>       Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip. Position Rest.
>      6.58188e+04    9.41710e+04   -7.10195e+05   -1.62296e+05    9.89235e+02
>        Potential Pressure (bar)
>     -6.92062e+05   -3.32594e+03
>
>
> And the stdout looks like this:
>
> Step= 2646, Dmax= 3.6e-03 nm, Epot= -6.92039e+05 Fmax= 5.12625e+03, atom=
> 1022
> Step= 2647, Dmax= 4.3e-03 nm, Epot= -6.92098e+05 Fmax= 3.72457e+03, atom=
> 1022
> Step= 2647, Dmax= 4.3e-03 nm, Epot= -6.92062e+05 Fmax= 1.51933e+03, atom=
> 1022
> Step= 2648, Dmax= 5.2e-03 nm, Epot= -6.92099e+05 Fmax= 4.25221e+03, atom=
> 1022
> Step= 2648, Dmax= 5.2e-03 nm, Epot= -6.92041e+05 Fmax= 6.45781e+03, atom=
> 1022
>
> The command for the mdrun was:
>
> mpirun -n 2 $gromacsPath/mdrun_mpi -c $path/3m71_minim.pdb -compact
> -deffnm $path/3m71_minim -s $path/3m71_minim_ion.tpr  -v
> 2>>$path/minLogErr 1>>$path/minLogOut
>
> Can you please tell me whats wrong?
>

When EM is done, mdrun prints very clear messages indicating convergence (or 
lack thereof) with information about maximum force and potential energy.  If 
you're not seeing this information, mdrun isn't done or somehow got killed or 
hung up.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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