Using amberFF and NAMD

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

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Dear NAMD users,

I'm trying to use NAMD /amberFF by following exactly what the amber
homepage says to do:
http://ambermd.org/namd/namd_amber.html
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
homepage.

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

Thanks a lot,
Cheers!

-- 
---------------------------------------------------------------------------------
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
90050-170
E-mail: ferbachega_at_gmail.com
---------------------------------------------------------------------------------

• Next message: Peter Freddolino: "Re: Simulation crashes during annealing the reverted all-atom structure"
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