RE: Fwd: running NAMD with AMBER inputs

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sun Sep 01 2019 - 14:50:36 CDT

No. The force fields are parameterized/validated with a cutoff in mind. Infinite cutoffs have their place, but it isn't an accuracy vs performance question.

-Josh

On 2019-09-01 12:20:05-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

---------- Forwarded message ---------
From: Rui Chen <rchen6_at_ualberta.ca<mailto:rchen6_at_ualberta.ca>>
Date: Sun, Sep 1, 2019 at 11:29 AM
Subject: running NAMD with AMBER inputs
To: AMBER Mailing List <AMBER_at_ambermd.org<mailto:AMBER_at_ambermd.org>>

Hello,
I am running MD simulation with AMBER inputs, please find attached my configuration file. Since in AMBER force field, the switching function is turning off, the result will be less accurate. I found a template from NAMD user's guide and another example, both of them have a cutoff value 9.0. If I increase the cutoff to a large number (say, 999), will I increase the accuracy of the simulation?
Looking forward to your feedback. Thank you.
Best regards,
Rui

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