[gmx-users] error in implicit MD

Justin Lemkul jalemkul at vt.edu
Tue Mar 6 14:09:03 CET 2018

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 

> 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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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