[gmx-users] Re: periodic molecule

Valentina valentina.erastova at durham.ac.uk
Wed Sep 18 15:57:11 CEST 2013

Bonds are harmonic. I can test it by restraining them? For purpose of testing
I can even make the topology bond to be 2.06, as in the input file. 

My system shouldn't be any different from a mice sheet, for instance. Both
have Metal - O bonds that continue through the sheet. What do you mean by
"the original geometry" - obv it shall be slightly changing through the MD.

Shall I be on Gromacs Dev sub-forum to get more insights on how the
periodic_molecule works? Or may be could I ask person who implemented that
part? I would really like to get it working in Gromacs, rather than having
to change the engine.

Thank you,

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