[gmx-users] Ethanol energies with CHARMM ff

Justin Lemkul jalemkul at vt.edu
Wed Jul 19 03:16:46 CEST 2017

On 7/18/17 1:28 PM, Sonia Milena Aguilera Segura wrote:
> Dear GROMACS users,
> I am running a 4 nm box of ethanol and once I finished the MD, I got the right T, P, density. However, I noticed that my energies are odd. After several trials with different parameters and box sizes I am getting a Total Energy between -1.2 to 0.6 KJ/mol (already normalizaed, Total energy/#molecules). I checked the potential energy at the end of minimization and this was around -65 kJ/mol. Then, I observed that during NVT equilibration my potential energy decreased to a value around -33 kJ/mol with a kinetic energy also around the same value (33 kJ/mol), and that's why my final total energies and, therefore, enthalpies are giving values around 0. I ran 

I don't understand how you're calculating your enthalpies.  The kinetic energy 
is irrelevant because it should cancel between the gas and liquid phases for a 
given temperature, so the dHvap value is <U_liq>/N + <U_gas> + RT

also simulations with water, isopropanol, and acetonitrile and I am getting 
values of -52, -206, and-48, which seem reasonable to me. My paremeters have 
been already discussed in a previous mail (please see acetonitrile

Reasonable based on...?


with CHARMM ff), and they seem to be right to be used with CHARMM ff. I am using 
version 2016.3 (I did the sa
>   me in 5.1.2), sd integrator, Berendsen barostat for equilibration and P-R for MD production. Any ideas of what should I look for or what can I be doing wrong?
> Thank you very much!!!,
> Sonia Aguilera
> PhD student


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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