[gmx-users] [CASS SPAM]Re: [CASS SPAM]Re: [CASS SPAM]Re: How to fix graphite layers?

Alex nedomacho at gmail.com
Thu Nov 29 09:59:16 CET 2018

> 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.


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