Re: [AMBER] Tethering water molecules in the receptor

From: George Tzotzos <gtzotzos.me.com>
Date: Sat, 04 Oct 2014 20:14:06 -0300

Thank you Jason,

In my simulations Iíve 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.

Iím reassured that I havenít 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 "evaporatingĒ.
>>
>> I havenít 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 ďtetheringĒ 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 donít 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 ďcapĒ, 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 canít use a periodic system instead.
>
> Of course itís also possible Iíve misunderstood what youíre 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
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