Re: Periodic cell basis too small for GridForce

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Mon May 28 2018 - 11:42:01 CDT

This usually happens because the size of the box of the density is much
larger than the system, and really just the empty space of the map is
outside the periodic cell, which is not actually a problem. You can avoid
this by trimming or cropping the map using the `volutil` plugin of VMD. You
can also turn the check off as the error suggests, setting either
`gridforcechecksize
off` in your config file (if using `gridforces` in your namd config )
or `mgridforcechecksize
0 off` (if using `mgridforces`).

On Sun, May 27, 2018 at 10:38 AM Carla Gómez Santiago <bscgs_at_leeds.ac.uk>
wrote:

> Hello everyone,
>
>
> Im new in MDFFs. Right now Im simulating a membrane receptor with extra
> constraints on the backbone of the receptor.
>
> During the equilibration, i get the following error message: FATAL ERROR:
> Warning: Periodic cell basis too small for Gridforce grid 0. Set
> gridforcechecksize off in configuration file to ignore.
>
> I tried increasing the Periodic cell basis in the previous .restart.xsc
> file and in the step5_assembly.namd.str however as the simulation moves
> on the shape of the box changes. Will that alter my results? I dont know
> what to do. Should I make changes in the Pressure?
>
> Any help highly appreciate
>
> Cheers,
>
>
> Carla
>

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