[gmx-users] Coupling groups
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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