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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 9 12:03:56 CEST 2012

On 9/04/2012 7:27 PM, James Starlight wrote:
> Mark,
>     If you make your layer boundaries perpendicular to some axis then
>     you can use position restraints on water oxygens that have
>     non-zero force constants only with respect to that axis. Then
>     relax the water position restraints before any others.
> Yes, I've thought about this to apply posres onto selected coordinates 
> to allow waters move only laterally relavitely protein-membrane-like 
> system. But this prevent to move water into the receptor interious as 
> well so it's not very good aproach.

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...

> Also I've thought about vary of the ref_t oprions wich I've defined 
> separatelly for protein_membrane layer and for water_ions. As I've 
> told I want to increase confoprmation sampling of my protein by means 
> of gradually temperature increasing. Could I rise only ref_t for the 
> protein_ccl4 layer with the apllied posres on the protetn (backbone 
> atoms) and ccl4 ( C atoms) during nvt equilibration while not changing 
> ref_t for water and ions ? Will my system be some unphysicall in that 
> case ?  Or as the alternative way could I decrease ref_t for the 
> water_ions layer in the end of nvt equilibration to allow water to 
> move out from the Ccl4 layer?

Please check your spelling. Attention to detail is very important in 
doing such simulations, and you don't want to create the impression your 
simulation settings might look similar to the above :-) 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...

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