[gmx-users] Regarding minimum size
Mark Abraham
mark.j.abraham at gmail.com
Tue Mar 13 16:38:11 CET 2018
Hi,
On Tue, Mar 13, 2018 at 4:11 PM Chhavi Yadav <cy1235 at nyu.edu> wrote:
> Hi,
>
> why is calling mdrunner twice a problem?
>
Because nobody wrote the code with that in mind. There's a lot of things
that are built around the assumption that mdrun will start, and then stop,
and nothing happens next.
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?
>
I literally have no idea. The only thing I do know is that this is not the
right way to solve your problem "randomly sampling coordinates", but I
don't know enough about what you're trying to do to say anything more
helpful. Is this test particle insertion, or what?
Mark
> 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 Biochemist
> <https://maps.google.com/?q=%3E%3E+Virginia+Tech+Department+of+Biochemist&entry=gmail&source=g>
> ry
> > > >>>>
> > > >>>> 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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