[gmx-users] Ethanol energies with CHARMM ff
Sonia Milena Aguilera Segura
sonia-milena.aguilera-segura at enscm.fr
Thu Jul 20 11:28:22 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...?
Currently I am not trying to calculate dHvap, only comparing the energies (Total energy/#molecules and enthalphy with -nmol and -fluct_props option for g_energy, that gives me enthalpies in kJ/mol). If I am not mistaken, in practice this enthalpy is calculated as the total energy (internal energy) plus de pV correction, all divided by the number of molecules in the system to give a value of enthalpy in kJ/mol. Is there any way to compare this energies against experimental values? For what I've understood, this value can be only comparable against a computational chemistry calculation (DFT, etc) to compare the total energy of the system. Please correct me if I am wrong.
When I say that the values I am getting seem reasonable I meant that they are all non-zero values, and moreover, without really know if the value I am getting correspond to any experimental value and/or ab initio calculation, at least they are all negative and they seem to show and correspond to the strength of the molecular interactions, e.g. isopropanol displays higher energies than water and acetonitrile, which kind of correspond to strength of their molecular interactions. Moreover, the problem comes when I see the values of ethanol. No matter what, this value shouldn't be zero. Or am I missing something?
Perhaps I should have started by asking the physical meaning of this values and the right approach to analyze the energies of the system. Is comparing the energies as described before a bad practice? Is computing the dHvap the only and right approach?. In this case I would also need to simulate the gas phase for my solvents, right?. However, all of them are liquid at 298. How can I simulate the gas phase at this T?
Thank you very much in advance,
>>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?
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