[gmx-users] Energy group exclusions

[#SUKRITI GUPTA#]

Thanks a lot for the reply.


Regards
Sukriti
[https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3]

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>



________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abraham at gmail.com>
Sent: Friday, December 16, 2016 5:39:45 AM
To: gmx-users at gromacs.org; gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Energy group exclusions

Hi,

As you've seen in
http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html#energy-group-exclusions
such exclusions are only for efficiency, which would make negligible impact
here. And anyway the bonds in your molecule probably generate nonbonded
exclusions within that molecule from the nrexcl moleculetype setting.

Mark

On Thu, 15 Dec 2016 17:11 #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg> wrote:

> Dear all,
>
> I have a system containing one charged molecule in bulk water and I have
> frozen the molecule at the centre of the box. I run energy minimization
> followed by equilibration by NPT for 100ps and finally NVT production run.
>
> I wanted to know if it is needed to use energy group exclusions as my
> system has only only frozen molecule so there won't be any atom - atom non
> bonded interaction anyways between 2 frozen atoms, however within this
> molecule I have 3 atoms, so will their non bonded interaction also cause
> unrealistic energy values?
>
> Thanks
>
> Sukriti Gupta
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