[gmx-users] Problem in mdrun

[Mark Abraham]

Hi,

Sounds like your simulation is just blowing up. I suggest you use a version
of GROMACS that isn't five years old ;-)

Mark

On Wed, 14 Dec 2016 21:01 tasneem kausar <tasneemkausar12 at gmail.com> wrote:

> Dear All
>
> I am performing MD simulation of protein and drug in Gromacs_4.5.4 using
> amber99SB force field with tip3p water model. I have successfully generated
> the tpr file for full MD simulation with two drugs. I have some other drugs
> to simulate with the same protein. Everything goes smoothly till the energy
> minimization giving a negative potential energy value. When I am try to run
> position restrain, mdrun is not generating any output. There is no error or
> warning massage. I have enough disk space of around 125 GB. I have tried
> mdrun at another PC and also at Gromacs_4.6.3.
>
> Here is my mdp file for position restrain.
> ;
> ;    User spoel (236)
> ;    Wed Nov  3 17:12:44 1993
> ;    Input file
> ;
> title               =  Yo
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> constraintalgorithm =  LINCS
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  50000    ; total 100 ps.
> nstcomm             =  1
> nstxout             =  500
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> coulombtype         =  PME
> rcoulomb            =  0.9
> rvdw                =  1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps            =  Protein    Non-protein
> tau_t               =  0.1    0.1
> ref_t               =  300    300
> ; Energy monitoring
> energygrps        =  Protein    Non-protein
> ; Pressure coupling is not on
> Pcoupl              =  no
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
> Kindly tell me where I am missing.
>
> Thanks in advance.
>
> With Regards
> Tasneem Kausar
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