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

[Ben Tam]

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.