[gmx-users] How to fix graphite layers?

高恺 gaokai161 at mails.ucas.ac.cn
Thu Nov 29 12:02:34 CET 2018

Your reply is very helpful to me.
Thank you Alex!

> -----Original Messages-----
> From: Alex <nedomacho at gmail.com>
> Sent Time: 2018-11-29 16:59:20 (Thursday)
> To: gmx-users at gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Re: Re: Re: How to fix graphite layers?
> > My current plan is to divide the two atoms into two groups and set the peripheral atoms to the frozen group in mdp file. I am not sure what the interaction between the frozen and active groups is. If I need to generate top files for each of these two groups, how should I tell the 'hot graphite' to be binded to the frozen graphite adjacent to it?
> >
> I was talking about restraints, which are not the same as freezing 
> atoms. Once again, if the difference is not clear, please read the 
> manual and also maybe something more general about particle-based 
> simulations. In general, I believe that freezing atoms as part of a 
> finite-temperature simulation is completely wrong and should be avoided 
> as much as possible.
> Alex
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