[gmx-users] error on graphene sheet simulation

[John Whittaker]

Hi,

That tutorial is not from the GROMACS team, it is provided by a user.

Anyway, something is wrong with your topology. The CHARMM forcefield used
in that tutorial has the atomtype CG2R61 available, so it should be
defined in your topology as long as you include the CHARMM36 forcefield.

Can you copy/paste the contents of your topology in a reply?

- John

> while going through your tutorial on graphene sheet i was facing an error.
> https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/
>
> NOTE 2 [file nvt.mdp]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.
>
> Setting the LD random seed to 164492569
> Generated 20503 of the 20503 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 17396 of the 20503 1-4 parameter combinations
>
> ERROR 1 [file GRA.itp, line 7]:
>   Atomtype CG2R61 not found
>
>
> There were 2 notes
>
> -------------------------------------------------------
> Program:     gmx grompp, version 2019.1
> Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1333)
>
> Fatal error:
> There was 1 error in input file(s)
>
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> can you give any suggestion what could have gone wrong...
> thanks
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