[gmx-users] Effect of bond constraints on equilibrium densities of equilibrated liquids

Miguel Caro miguel.caro at aalto.fi
Fri Apr 15 17:56:36 CEST 2016

Apologies, the graph didn't show up. It can be viewed here:



On 2016-04-15 18:51, Miguel Caro wrote:
> Hi all,
> I am running some test calculations with acetonitrile/water mixtures
> using the GAFF topologies as available from virtualchemistry.org (by the
> way, thanks for this great resource). I obtain equilibrium densities
> from averages over different independent configurations after 1 ns
> equilibration periods (298 K, 1 bar, 400 water molecules and 200
> acetonitrile molecules at the end points). The equilibrium density I
> obtain for pure acetonitrile is larger than that reported on the website
> for GAFF
> (http://virtualchemistry.org/molecule.php?filename=acetonitrile.zmat)
> and slightly closer to the experimental value of 0.78 g/cm^3: it is
> about 0.8 g/cm^3 for me compared to 0.73 g/cm^3 from the reference
> calculation. I hope the graph copy-pasted below shows up on my email, to
> help illustrate the issue (each data point is one configuration
> equilibrated for 1ns). Going to the JCTC paper referenced on the website
> (Caleman et al. JCTC 8, 61 [2012]), it appears unless I'm mistaken that
> the reference results were obtained with constrained bonds (Table 1 on
> that paper, "LIQ" item). However, I am allowing all bonds to vibrate in
> my simulation (with appropriate small time steps).
> My question is whether I can/should expect the difference in predicted
> density to originate from the lifted bond constraints, or is there
> something else flawed about how I'm running this simulation. I.e.,
> should I run longer simulations, calculate for each configuration the
> average density over the simulated trajectory instead of taking the
> final density value, etc.?
> Many thanks for you help,
> Miguel

*Dr. Miguel Caro*
/Postdoctoral researcher/
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: *mcaroba at gmail.com*
Work: *miguel.caro at aalto.fi*
Website: http://mcaroba.dyndns.org

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