Thank you Jason,
In my simulations I’ve prepared a topology file which includes a water molecule that is deemed to be conserved. In some simulations ( > 60ns) I find that the water molecule diffuses out of the binding pocket.
I’m reassured that I haven’t overlooked something important in preparing for the simulations.
Cheers
George
On 4Oct, 2014, at 6:09 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Oct 4, 2014, at 3:37 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I read in Amber12 manual (Section 5.8.1, p.132)
>>
>> leap recognizes water if the residue name is WAT or HOH. In later simulations, they may have to be tethered (more or less strongly) to their original positions to prevent them from "evaporating”.
>>
>> I haven’t been able to find a way to tether WAT during long production MD simulations. Any ideas how to do so would be greatly appreciated.
>
> Note that “tethering” is unnecessary in most modern simulations employing explicit solvent. Evaporation is really only an issue when you are simulating a microscopic droplet, in which case the surface area-to-volume ratio is _very_ large and surface effects (including evaporation) are critically important.
>
> If you want to prevent evaporation, then you likely want to simulate a bulk solution phase. In this case, you simply apply periodic boundary conditions to your system and don’t worry about it, since there *is* no surface and therefore no evaporation.
>
> In the days before people used PBC, they would often employ a so-called solvent “cap”, which I believe is basically a restraining potential that prevented water from moving too far away from the solvent. You can still use caps in Amber, I believe, but you should make sure you really need this and can’t use a periodic system instead.
>
> Of course it’s also possible I’ve misunderstood what you’re trying to do, in which case perhaps someone else will be able to figure it out or you can clarify a bit more.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Sat Oct 04 2014 - 16:30:02 PDT
