Using amberFF and NAMD

From: José Fernando Ruggiero Bachega (
Date: Fri Jul 19 2019 - 12:07:54 CDT

Dear NAMD users,

I'm trying to use NAMD /amberFF by following exactly what the amber
homepage says to do:
But I got very weird results.

I'm not applying any kind restriction but the water molecules look like
they were restricted by some harmonic potential. It's totally different
from the behavior that I see in a similar system using CHARMM.

I tried several systems, including those available at the amber tutorial

Could anyone share an example using NAMD /amberFF that works properly?

Thanks a lot,

José Fernando Ruggiero Bachega, PhD
Universidade Federal de Ciências da Saúde de Porto Alegre – UFCSPA
Rua Sarmento Leite, 245 - Porto Alegre, Rio Grande do Sul, Brasil - CEP

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