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<div>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,<br/>
there might be better suggestions though.</div>
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<div>Stephan</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Donnerstag, 30. Mai 2013 um 20:48 Uhr<br/>
<b>Von:</b> "Dejun Lin" <dejun.lin@gmail.com><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> [gmx-users] Free energy calculation: merge the topology of 2 molecules</div>
<div name="quoted-content">Hi all,<br/>
<br/>
I'm trying to set-up a free energy calculation where a molecule has +2<br/>
charge in it's native state (state A) and no charge in the mutant (state<br/>
B). Since the molecule has net +2 charge, I have to add counter-ions to<br/>
neutralize the system in state A. But in order to transform it to state B<br/>
and still maintain a neutral system, the counter-ions have to be<br/>
transformed too. I tried only transforming only the target molecule not the<br/>
ions but the simulation crashes very quickly.<br/>
<br/>
I searched the gmx-users archives and found some suggestion about merging<br/>
the topology definition of ions into that of the molecule under one<br/>
[moleculetype] section. I tried that but mdrun warned me with tons of<br/>
"inconsistent shift":<br/>
<br/>
There were 2 inconsistent shifts. Check your topology<br/>
There were 18 inconsistent shifts. Check your topology<br/>
There were 16 inconsistent shifts. Check your topology<br/>
There were 12 inconsistent shifts. Check your topology<br/>
There were 16 inconsistent shifts. Check your topology<br/>
...<br/>
<br/>
and the simulation can't be run in parallel because mdrun would just quick<br/>
and complain about not being able to do domain decomposition:<br/>
<br/>
There is no domain decomposition for 16 nodes that is compatible with the<br/>
given box and a minimum cell size of 29.6188 nm<br/>
<br/>
I guess the issue is Gromacs thinks those counter-ions belongs chemically<br/>
to the target molecule although they are actually not in close proximity in<br/>
space, which mess up the DD. partition.<br/>
<br/>
I wonder if there's a way to get around that.<br/>
<br/>
Thanks,<br/>
Dejun<br/>
--<br/>
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