[gmx-users] NVT Equilibration

Matthew Zwier mczwier at gmail.com
Thu Oct 6 23:09:59 CEST 2011

Concur.  I just used this approach to equilibrate a box of
water/acetonitrile.  If your box shrinks too much, you can probably
use editconf and genbox to replicate the equilibrated box into a
larger box of arbitrary size and shape.


On Thu, Oct 6, 2011 at 4:36 PM, Dallas Warren <Dallas.Warren at monash.edu> wrote:
> Ravi, not entirely sure what you are actually doing / aiming to do, but another option is to run the system NPT, which means the box size will scale to give the correct pressure / density, then you take that and run your NVT run.  But that means you will end up with possibly a substantially smaller box, which may be an issue.  But, closer you are to the correct starting point when you build the box the better.
> Catch ya,
> Dr. Dallas Warren
> Medicinal Chemistry and Drug Action
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.

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