Hi,
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:
WATNAM = 'TIP3', OWTNM = 'OH2',
Hope this helps,
-Dan
On Wed, Nov 28, 2018 at 3:17 PM Stejskal, Lenka
<lenka.stejskal.15.ucl.ac.uk> 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
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Received on Mon Dec 03 2018 - 12:30:03 PST
