[gmx-users] Re: Energy minimization has stopped....

[Justin Lemkul]

On 11/5/13 7:19 AM, Kalyanashis wrote:
> I have given my .mdp file,
> ; title             =  trp_drg
> warning             =  10
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002 ; ps !
> nsteps              =  1000000 ; total 2000.0 ps.
> nstcomm             =  100
> nstxout             =  250 ; ouput coordinates every 0.5 ps
> nstvout             =  1000 ; output velocities every 2.0 ps
> nstfout             =  0
> nstlog              =  100
> nstenergy           =  100
> nstlist             =  100
> ns_type             =  grid
> rlist               =  1.0
> coulombtype         =  PME
> rcoulomb            =  1.0
> vdwtype             =  cut-off
> rvdw                =  1.0
> fourierspacing      =  0.12
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  6
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
> ; Berendsen temparature coupling is on
> Tcoupl      =  berendsen
> tau_t               =  1.0    1.0    -0.1      1.0   1.0
> tc_grps             =  SOL    NA     protein   OMP   CL
> ref_t               =  300    300    300       300   300

These settings make no sense.  Please read 
http://www.gromacs.org/Documentation/Terminology/Thermostats.

> ; Pressure coupling is on
> pcoupl              =  berendsen ; Use Parrinello-Rahman for research work
> pcoupltype          =  isotropic ; Use semiisotropic when working with
> membranes
> tau_p               =  2.0
> compressibility     =  4.5e-5
> ref_p               =  1.0
> refcoord-scaling    =  all
> ; Generate velocites is on at 300 K.
> gen_vel             = yes
> gen_temp            = 300.0
> gen_seed            = 173529
>
>
> And It is a large protein system containing drug molecule and the atoms of
> whole system is near about 16000.
> As I did not get any .gro file, thus the MD run was not properly finished.
> Please suggest me the probable source this kind error.

The run crashes because your energy minimization effectively failed.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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