[gmx-users] Re: periodic molecule

[Valentina]

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,
V

--
View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011288.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.