Re: NAMD configuration file

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Thu Aug 29 2019 - 19:52:03 CDT

A quick glance of the user manual would answer your question.

V

On Thu, Aug 29, 2019 at 8:33 PM Rui Chen <rchen6_at_ualberta.ca<mailto:rchen6_at_ualberta.ca>> wrote:
Hello,

Is there anyone help me solve this problem? Thank you in advance.

Best regards,
Rui

On Tue, Aug 27, 2019 at 2:55 PM Rui Chen <rchen6_at_ualberta.ca<mailto:rchen6_at_ualberta.ca>> wrote:
Hello,

I am running MD simulation using NAMD. The input files were prepared from AMBER force field. I realized there are some differences between AMBER and CHARMM force fields. "The most important difference concerns the 1-4 non-bonded charge-charge interactions, which are scaled by a factor of 0.833 in the AMBER force field and scaled by a factor of 1.0 in the CHARMM force field." I am following a charmm force field configuration file. Is there any other parameters that I need to change? For example, in AMBER force field, switches off, rather than scaling.

If I forget to set the 1-4 scaling to 0.8333 (I used 1.0), how it will influence the system? Thank you.

Best regards,
Rui

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