Re: [AMBER] Total energy of system is positive

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 29 Dec 2014 18:23:49 -0500

On Mon, Dec 29, 2014 at 5:29 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:

> I slightly disagree with Jason here.
>
> 0.5% Choline Lactate solution in water, is mostly water, right? There is
> no way that has a positive energy.
>
> If by 0.5% choline lactate you mean 99.5% choline lactate, 0.5% water,
> then it might be a different story. In any case, an ionic liquid energy
> would be cominated by electrostatic attraction between molecules of
> opposite charge, so I would also expect negative energies all around.
>

​But what's the minimum energy of a single Choline molecule? It is quite
possibly positive, in which case adding a lot of them could result in a
very positive energy (if attractive intermolecular forces cannot fully
"offset" the positive energy of the choline molecule itself). But this
doesn't indicate a problem in itself -- only energy differences hold any
meaning in molecular mechanical simulations.

However, bulk water has a very strongly negative overall energy, so I would
agree that a 99.5% water -- 0.5% choline mixture should be negative, and a
positive energy would indicate a problematic system (perhaps it is overly
compressed). I admit to reading the OP as 99.5% choline lactate + 0.5%
water, then 99% choline lactate and 1% water (this would make sense given
the trend of decreasing total energies).

If the system is mostly water, the energy should be negative and you should
look for a problem. If it is mostly choline lactate, then it could very
well be mostly positive.

At the end of the day, a positive energy does not, by itself, indicate any
kind of problem (nor does a negative energy mean that there are no
problems).

​HTH,
Jason​

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 29 2014 - 15:30:02 PST
Custom Search