[gmx-users] error in implicit MD

[Justin Lemkul]

On 3/6/18 5:39 AM, Vishwambhar Bhandare wrote:
> Dear gromacs user,
>
> I am trying implicit simulation on my system.
> I am getting the error during equilibration as,
> "Can't do GB electrostatics; the implicit_genborn_params section of the
> forcefield is missing parameters for 19 atomtypes or they might be
> negative".

This means the force field you chose doesn't have the requisite GB 
parameters.

> The Version I am using is 4.5.4
>
> If I use the latest version of gromacs 2016.4,
> i get error as copied below,
>
> ERROR 1 [file em.mdp]:
>    With Verlet lists only full pbc or pbc=xy with walls is supported

You need to use cutoff-scheme = group to make use of a non-periodic system.

> my mdp file is enclosed for reference.

For future reference, the mailing list does not accept attachments. 
Either copy and paste the content into your email or upload the file to 
a file-sharing service and provide a URL. In this case, though, an .mdp 
is not necessary because the errors are very clear.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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