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

[Mark Abraham]

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
>
> 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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