[gmx-users] Re: Simulation in the high temperature conditions

James Starlight jmsstarlight at gmail.com
Mon Apr 9 13:48:00 CEST 2012


> Assuming you're raising your temperature during equilibration and then
> running at high temperature, then you don't want water moving into the
> receptor interior during equilibration for the same reason you didn't want
> water moving into the CCl4. And you're going to run further equilibration
> after taking off all the restraints anyway, right? And if water moves into
> the receptor interior, then it probably does that under high-temperature
> equilibrium conditions...

It is that I want to prevent movement of water into Ccl4 layer (that is
drive by the increased temperature and have not been present in the natural
conditions) but allow it to move into the receptor interiour ( that is
normally observed experimentally). So the posres application may prevent
water to move both into the receptor and Ccl4 so this aproach could not be
useful in my case, couldn't it ?

> On point, the reference temperature has little to do with whether phases
> diffuse into (or out of) each other, and lots to do with what ensemble you
> might be sampling. The actual temperature controls the rate of such
> diffusion, of course, but if the non-bonded interactions allow for
> intermixing, then you'll get some degree of that regardless of any other
> setting. You'd be well advised to check that your CCl4-water boundary
> behaves acceptably before you invest in the protein simulation...

Specifically I've desided to rise temperature of my system to increase
conformation sampling of the protein surrounded of the interiour. For this
I've devided my system on several parts to couple to separate thermostates.
One part is the protein and CCl4 layer wich mimick the membrane and another
part is the sorrounded water ( SOL), internal water ( wich may present in
the protein interiour transitory but never in the Ccl4 layer) and IONS (
wich are always in the SOL layer). In order that increase the rate of
conformation sampling I've gradually increased ref_t of each t_group. In
part this result in evaporation of water and some of that water has moved
in Ccl4 layer. So its intresting for me might  I set ref_t for water_ions
group as the specified value ( ref_t= 310 k) and gradually increase only
ref_t for the protein_ccl4 group in the annealing manner. As the
consequence I want to prevent evaporation of the water but maintain of the
overal temperature high of my system tp increase sampling of the protein
conformation ?

I inderstand that such aproach is very unphysical but aplication of the
posres and other tricks are from this theme but works good in some cases :)


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