Re: [AMBER] Minimisation and periodic boundaries.

From: Daniel Roe <>
Date: Mon, 3 Dec 2018 15:21:16 -0500


If you have periodic boundary conditions you should be setting ntb,
and if you are dealing with a membrane system you likely want ntb = 2
(along with a barostat) for constant pressure. Also, if you're using
CHARMM parameters in Amber you need to make sure that your cutoffs and
things like force switch (fswitch) are appropriately set - I'm not
sure if CHARMM-GUI sets these things or not. Also note that if you're
using CHARMM residue and atom names you need the following to ensure
SHAKE works properly:


Hope this helps,

On Wed, Nov 28, 2018 at 3:17 PM Stejskal, Lenka
<> wrote:
> Dear Sally,
> Thank you very much for your reply. I am planning to use CHARMM ff for this simulation.
> May I ask why is it suitable not to set periodic boundary during a minimisation using this ff?
> Thank you
> Lenka
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Mon Dec 03 2018 - 12:30:03 PST
Custom Search