[gmx-users] Problem with Group and Verlet cut -off scheme

[Mark Abraham]

Hi,

Why does your topology have an interaction between atoms that are ~6 nm
apart?

Mark

On Fri, Jul 8, 2016 at 12:37 PM Ben Tam <btam125 at hotmail.co.uk> wrote:

> Hi Mark,
>
>
> Thank you for your reply and your suggestion. Now I get it working, I have
> another problem. This error pops up when I do:
>
>
> gmx mdrun -table table6-12.xvg -tablep table_Mg_O4.xvg
>
>
> This is the error I am getting. I am trying to understand it, but I don't
> understand how to solve it:
>
>
> Fatal error:
> There is no domain decomposition for 6 ranks that is compatible with the
> given box and a minimum cell size of 6.75819 nm
> Change the number of ranks or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
>
> Thanks for your help,
>
>
> Best regards,
>
>
> Ben
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: 07 July 2016 15:07
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem with Group and Verlet cut -off scheme
>
> Hi,
>
>
> On Thu, Jul 7, 2016 at 3:44 PM Ben Tam <btam125 at hotmail.co.uk> wrote:
>
> > Dear Gromacs users,
> >
> >
> > Thank you very reading. I am trying to run a simulation that requires me
> > to use lennard jones and buckingham potential mix,
>
>
> That's often tricky to get right, because you still need VDW combination
> rules that work for all pairs of atom types that might be within an
> interaction radius (and probably slightly breaks any dispersion correction
> also). Then you have to express that as energy groups to get the tables to
> work (without running out of energy groups, IIRC max 128).
>
> thus I have to make my own tabulated table .xvg list. However here is my
> > problem, because Verlet does not support tabulated table so I have to use
> > group scheme. But here is the error message I am getting :
> >
> >
> > Fatal error:
> > The largest charge group contains 574 atoms. The maximum is 32.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> Errors - Gromacs<http://www.gromacs.org/Documentation/Errors>
> www.gromacs.org
> Atom index n in position_restraints out of bounds . A common problem is
> placing position restraint files for multiple molecules out of order.
> Recall that a position ...
>
>
>
> >
> > My simulation is a single crystal structure. Thus my question is:
> >
> >
> > 1) is it possible to change the charge group? if so, how? as I read the
> > manual seems it is not possible.
> >
>
> You specified the charge groups in your molecule's [atoms] section, so you
> can select a different setup, e.g. one charge group per atom (and your
> neighbourlist should likely be set up to have a buffer)
>
>
> > 2) if I am using tabulated table, do I have to make a .xvg file for all
> > interacting molecule (because I just need to change one interaction into
> > buckingham potential)
> >
>
> For historical reasons, each energygroup pair needs to either use the
> default interaction type, or replaced with a table.
>
> Mark
>
>
> > Thank you very much.
> >
> >
> > Best regards,
> >
> >
> > Ben
> > --
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