[gmx-users] MD run failed..

[HANNIBAL LECTER]

Exactly. The reason I asked....

On Fri, Feb 20, 2015 at 1:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/20/15 1:01 PM, HANNIBAL LECTER wrote:
>
>> Just out of curiosity what does -0.1 actually mean?
>>
>>
> It means someone made a mistake :)  It's not physically sensible.  tau-t
> should be a positive decimal or -1 to turn off coupling for that group.
> Using -0.1 doesn't make any sense.  It's probably the primary reason for
> failure here.
>
> -Justin
>
>
>  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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> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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