[gmx-users] Coupling groups

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 6 12:44:58 CET 2012

On 6/03/2012 10:40 PM, Steven Neumann wrote:
> On Tue, Mar 6, 2012 at 11:35 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 6/03/2012 8:21 PM, Steven Neumann wrote:
>         Dear Gmx Users,
>         I am running my protein with ligand. at the begining of my
>         simulation the protein is far away from the ligand. Then in
>         about 5-10 ns my ligand binds to the protein surface remaining
>         there for rest 90-95 ns. Would you adjust coupling groups in
>         thermostat as:
>         a) Protein_LIg and Water_and_ions
>         b) Protein Water_ions_LIG
>         c) Protein LIG Water_ions
>     I'd consider a single coupling group before any of those. See
>     final part of manual 3.4.8 and ref therein. c) is unsound because
>     the ligand is likely too small. The lack of T-group atom
>     contiguity in a) might be an issue, I'm not sure. b) is probably
>     what people do, but you know this from your literature searching
>     about similar work, right? :-)
> Well...I used a) approach as Ligand becaome a part of the protein 
> quite fast.

Sure, but if the path that took it there might be unsound, then you 
can't refute the argument that the fact that that path occurred might be 
a numerical artefact.

> The b) just was my own tought as at the begining of the simulation is 
> in water only, however just for 500 ps as far as I see out of 100ns. 
> How would you tackle this?

Didn't I answer this already? :-)

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