[gmx-users] Regarding minimum size
Chhavi Yadav
cy1235 at nyu.edu
Tue Mar 13 16:10:17 CET 2018
Hi,
why is calling mdrunner twice a problem?
I get the correct value when mdrunner runs the first time. Why do I get the
error only during the second time considering I am not anyway doing any
settings during both the times?
Thanks,
Chhavi
On Mon, Mar 12, 2018 at 6:24 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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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