[gmx-users] Pre-equilibrating the solvent before solvating the solute

[Justin Lemkul]

On 12/17/19 4:43 PM, D. Yousefi wrote:
> I want to perform an MD simulation at high-temperature, and I need to
> pre-equilibrate water molecules at that temperature before solvating my
> protein so that the solvent reaches the correct density. What is the
> appropriate way of doing this? As the first step, should I define my box
> with water molecules only and then equilibrate the system? If so, how can I
> solvate my protein in this system?

You can do this one of two ways - either (1) prepare a box of water and 
run at the higher temperature, then use that as input for gmx solvate 
-cs or (2) just solvate your system with the existing spc216.gro and 
equilibrate the whole system at the higher temperature, which you will 
need to do anyway. I don't see a clear benefit in (1) over (2).

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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