Thanks for your reply, Stephan. Did the molecule you worked with have any atoms that are isolated (non-bonded) to the others? Was the equilibration run in your 1st case just a way to recruit those isolated atoms to the others in the same molecule? I suspect I might need to add artificial bond to connect the counter-ions to the target molecule.
In the 2nd case you mentioned, I'm not sure why it would work for you but not me because I essentially have every atoms in their single charge groups. Thanks, Dejun 2013/5/30 lloyd riggs <lloyd.ri...@gmx.ch> > I've had 2 problems like this. 1 was solved by doing all eq to a good > degree first in one thread, then the domain decomposition worked in 8 or > 16...the secound I had to break down the charge groups in the .itp (cg) > into smaller charge groups and it worked, > there might be better suggestions though. > > Stephan > > *Gesendet:* Donnerstag, 30. Mai 2013 um 20:48 Uhr > *Von:* "Dejun Lin" <dejun....@gmail.com> > *An:* gmx-users@gromacs.org > *Betreff:* [gmx-users] Free energy calculation: merge the topology of 2 > molecules > Hi all, > > I'm trying to set-up a free energy calculation where a molecule has +2 > charge in it's native state (state A) and no charge in the mutant (state > B). Since the molecule has net +2 charge, I have to add counter-ions to > neutralize the system in state A. But in order to transform it to state B > and still maintain a neutral system, the counter-ions have to be > transformed too. I tried only transforming only the target molecule not the > ions but the simulation crashes very quickly. > > I searched the gmx-users archives and found some suggestion about merging > the topology definition of ions into that of the molecule under one > [moleculetype] section. I tried that but mdrun warned me with tons of > "inconsistent shift": > > There were 2 inconsistent shifts. Check your topology > There were 18 inconsistent shifts. Check your topology > There were 16 inconsistent shifts. Check your topology > There were 12 inconsistent shifts. Check your topology > There were 16 inconsistent shifts. Check your topology > ... > > and the simulation can't be run in parallel because mdrun would just quick > and complain about not being able to do domain decomposition: > > There is no domain decomposition for 16 nodes that is compatible with the > given box and a minimum cell size of 29.6188 nm > > I guess the issue is Gromacs thinks those counter-ions belongs chemically > to the target molecule although they are actually not in close proximity in > space, which mess up the DD. partition. > > I wonder if there's a way to get around that. > > Thanks, > Dejun > -- > 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 > > -- > 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 > -- 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
