[gmx-users] Free energy calculation: merge the topology of 2 molecules

[Dejun Lin]

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.riggs at 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.lin at gmail.com>
> *An:* gmx-users at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>