[gmx-users] MD run failed..

[HANNIBAL LECTER]

Just out of curiosity what does -0.1 actually mean?

On Fri, Feb 20, 2015 at 8:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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