[gmx-users] MD run failed..

[Justin Lemkul]

On 2/20/15 6:51 AM, Kalyanashis Jana wrote:
> Dear all,
> I am doing an MD simulation of a protein system. Energy minimization step
> has been completed smoothly but the position restraint MD run is not
> running properly(after 500-900 steps have been stopped automatically). Even
> it has not shown any error or anything. I have used a drug molecule in the
> cavity of the active site.
> When the box size was 10 X 12 X 25, it was run only 100 steps and with 15 X
> 15 X 28 box size it was run 500-900 steps. I could not understand what is
> the problem. Can anyone please help me?
>
> The pr.mdp file is
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.001 ; ps !
> nsteps              =  1000000 ; total 1000.0 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
> ; V-rescale temparature coupling is on
> Tcoupl                =  V-rescale
> tau_t               =  1.0    1.0    -0.1      1.0   1.0
> tc_grps             =  SOL    NA     protein   DRG   CL
> ref_t               =  300    300    300       300   300

This thermostat setup is nonsensical.

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do

-Justin

> ; 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
>
>
> Thanks in advance,
> Kalyanashis Jana.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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