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. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
