[gmx-users] Coupling groups

Steven Neumann s.neumann08 at gmail.com
Tue Mar 6 12:53:58 CET 2012

On Tue, Mar 6, 2012 at 11:44 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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? :-)

My ligand will stack to everything and I put it around my protein in
different positions and run separate simulations. Then the final
coordinates will be chosen for binding free energy calculations (umbrella
sampling) so think it is better approach.

> Mark
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