[gmx-users] Regarding minimum size

[Chhavi Yadav]

I wrote this code and was running the debugger:


int main(int argc, char *argv[]) {


    int rc;
    MD mdrunner;
    rc = mdrunner.mainFunction(argc, argv);
    printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);

    mdrunner.epot = 0;

    t_state *t = mdrunner.globalState.get();
    t->x[0][0] = 10.0;
    t->x[0][1] = 10.0;
    t->x[0][2] = 10.0;


    rc = mdrunner.mainFunction(argc, argv);
    printf("Potential Energy from integrator: %.6f\n", mdrunner.epot);

    return rc;

}

OUTPUT:

Reading file 1aki/1AKI.tpr, VERSION
2018-dev-20180223-a989b355c-dirty-unknown (single precision)

NOTE: disabling dynamic load balancing as it is not supported in reruns.

No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
No option -multi
Using 8 MPI threads
starting md rerun 'LYSOZYME', reading coordinates from input trajectory
'1aki/1AKI.gro'

Reading frames from gro file 'LYSOZYME;', 1960 atoms.

Reading frame       0 time    0.000
WARNING: Some frames do not contain velocities.
         Ekin, temperature and pressure are incorrect,
         the virial will be incorrect when constraints are present.


Last frame          0 time    0.000

               Core t (s)   Wall t (s)        (%)
       Time:        0.961        0.120      800.0
                 (ns/day)    (hour/ns)
Performance:        0.719       33.377
Potential Energy from integrator: -8519.961914

NOTE: disabling dynamic load balancing as it is not supported in reruns.


-------------------------------------------------------
Program:     GROMACS, version 2018-dev-20180308-65a7ab86c-dirty-unknown
Source file: src/gromacs/domdec/domdec.cpp (line 6571)
MPI rank:    0 (out of 8)

Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the
given
box and a minimum cell size of 5.81734 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

On Mon, Mar 12, 2018 at 2:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/12/18 2:05 PM, Srinivasa Ramisetti wrote:
>
>> I think the minimum coordinates are (0,0,0)
>>
>>
> Not really. GROMACS will accept negative coordinates and then re-wrap them
> into the periodic box with its origin at (0,0,0).
>
> An actual error message and full command from the OP would be helpful here.
>
> -Justin
>
>
> Srinivasa
>> On 12/03/2018 18:01, Chhavi Yadav wrote:
>>
>>> Hi Justin,
>>> Thanks for the reply.
>>>
>>> I meant this : In our application, we need to randomly sample coordinates
>>> for atoms. When we were doing that, we got an error message for one of
>>> the
>>> random coordinate samples because the sample coordinate was smaller than
>>> the minimum coordinates. What is this minimum coordinate and how can I
>>> find
>>> its value?
>>>
>>> I hope the question is clear now.
>>>
>>> Thanks,
>>> Chhavi
>>>
>>> On Mon, Mar 12, 2018 at 1:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>> On 3/12/18 1:30 PM, Chhavi Yadav wrote:
>>>>
>>>> Hello,
>>>>>
>>>>> This is regarding the minimum size or resolution used in gromacs for
>>>>> sampling coordinates of atoms. I know that the maximum size is the
>>>>> matrix
>>>>> box. Can someone please let me know what the minimum is?
>>>>>
>>>>> I'm not sure if this is the answer to your question, but GROMACS can
>>>> perform MD for any number of particles. The minimum box size depends on
>>>> the
>>>> cutoff values required for a given force field, as required by the
>>>> minimum
>>>> image convention, but one could simulate even a few atoms in the gas
>>>> phase
>>>> if desired.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>>
>>>> ==================================================
>>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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