[gmx-users] Regarding minimum size
Mark Abraham
mark.j.abraham at gmail.com
Mon Mar 12 23:25:04 CET 2018
Hi,
That's not a valid way to use these components. Whatever you're trying to
do shouldn't be attempted by trying to call mdrunner.mainFunction() twice.
Mark
On Mon, Mar 12, 2018 at 9:54 PM Chhavi Yadav <cy1235 at nyu.edu> wrote:
> 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
> >>>>
> >>>> ==================================================
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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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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