Re: [gmx-users] Enthalpy of Vaporization

2015-10-06 Thread Justin Lemkul
On 10/5/15 11:30 PM, Pallavi Banerjee wrote: My system is one molecule of Propanamide. I need to see if my force field makes the molecule water soluble or not, for which I would need its cohesive energy, and this in turn would require the heat of vaporization. So, I should include the total

Re: [gmx-users] Enthalpy of Vaporization

2015-10-05 Thread Justin Lemkul
On 10/5/15 1:50 PM, Pallavi Banerjee wrote: Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the total potential energy of the system (which is given by g_energy) minus the total bonded potential energy

Re: [gmx-users] Enthalpy of Vaporization

2015-10-05 Thread Pallavi Banerjee
Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the total potential energy of the system (which is given by g_energy) minus the total bonded potential energy (bonds+angles+dihedrals). Am I thinking right? Thanks.

Re: [gmx-users] Enthalpy of Vaporization

2015-10-05 Thread Justin Lemkul
On 10/5/15 2:01 PM, Rasoul Nasiri wrote: On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul wrote: On 10/5/15 1:50 PM, Pallavi Banerjee wrote: Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the

Re: [gmx-users] Enthalpy of Vaporization

2015-10-05 Thread Rasoul Nasiri
On Mon, Oct 5, 2015 at 7:03 PM, Justin Lemkul wrote: > > > On 10/5/15 2:01 PM, Rasoul Nasiri wrote: > >> On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul wrote: >> >> >>> >>> On 10/5/15 1:50 PM, Pallavi Banerjee wrote: >>> >>> Correct me if I am wrong, please.

Re: [gmx-users] Enthalpy of Vaporization

2015-10-05 Thread Pallavi Banerjee
My system is one molecule of Propanamide. I need to see if my force field makes the molecule water soluble or not, for which I would need its cohesive energy, and this in turn would require the heat of vaporization. So, I should include the total potential energy for both gas and liquid phase in

[gmx-users] Enthalpy of Vaporization

2015-10-05 Thread Pallavi Banerjee
Hello Users, I need to calculate the cohesive energy for my system, for which the enthalpy of vaporization is needed. Am I right to assume that just the non-bonded interaction energy (potential energy) is required to calculate the enthalpy of vaporization ? Many Thanks! -Pallavi Banerjee --

Re: [gmx-users] Enthalpy of Vaporization

2015-10-05 Thread Justin Lemkul
On 10/5/15 10:53 AM, Pallavi Banerjee wrote: Hello Users, I need to calculate the cohesive energy for my system, for which the enthalpy of vaporization is needed. Am I right to assume that just the non-bonded interaction energy (potential energy) is required to calculate the enthalpy of

Re: [gmx-users] Enthalpy of Vaporization

2015-10-05 Thread Rasoul Nasiri
This non-zero value becomes quite significant if you are dealing with highly flexible molecules - Internal molecular dynamics effects are different in the gas and liquid phases. Rasoul On Mon, Oct 5, 2015 at 3:53 PM, Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hello