Re: [gmx-users] Surface Tension Calculation

Hi, Dan, Thanks for your response. The interfacial tensions I get from gmx energy is way larger than the typical surface free energy of solid. So I suspect the freeze command may have generated some artifacts and I need to find a better force field. -- Gromacs Users mailing list * Please search

Re: [gmx-users] Surface Tension Calculation

Hi Lei, 1. In the Gromacs manual you can find the formula that the software uses to calculate surface tension. It is just based on a few components of the pressure tensor, so I imagine you can just use gmx energy (or g_energy depending on the version of Gromacs you are using). 2. Freezing doesn't

[gmx-users] Surface Tension Calculation

Hi, gmx users, I have some questions regarding the surface tension calculation in gromacs. I was running simulations about interface between phase 1 (solid) and phase 2 (liquid). In my production run, the phase 1 molecules are frozen and I need to calculate the interfacial tension between phase 1

Re: [gmx-users] Surface tension calculation for organic monolayer

Create another residue that has a missing hydrogen in the -OH group so that your acid is COO- instead of COOH. Then add this acid along with the protonated one in different proportions and then add enough hydrogen atoms to account for the undercoordinated oxygens. That's one way to do it, there

Re: [gmx-users] Surface tension calculation for organic monolayer

Yes but my acid is in protonated form. > On 13 Jul 2016, at 17:42, Evan Lowry wrote: > > Dr. van der Spoel is correct. If you don't take into account the > protonation state, your calculation may likely be incorrect. The pH can > have a notable effect on

Re: [gmx-users] Surface tension calculation for organic monolayer

Dr. van der Spoel is correct. If you don't take into account the protonation state, your calculation may likely be incorrect. The pH can have a notable effect on interfacial/surfactant systems. Evan L. Dear Spoel, I am using the protonated form of cis-pinonic acid which means head group is COOH.

Re: [gmx-users] Surface tension calculation for organic monolayer

Dear Spoel, I am using the protonated form of cis-pinonic acid which means head group is COOH. I tried many other surface active molecules but never manage to estimate the lower surface tension than water. Is there anyone here that did the MD simulations with surface active molecules on water

Re: [gmx-users] Surface tension calculation for organic monolayer

On 07/07/16 17:51, gozde ergin wrote: Dear Spoel, Thanks for your respond. For this simulations I used acids however I got the similar results when I used alcohol (pK values are lower than acids). I doubt this error coming from the pH effects. But how could i get the protonated molecules

Re: [gmx-users] Surface tension calculation for organic monolayer

Few things to check: Do you observe that the cis-pinonic acid or alcohol forms a monolayer at the water-vacuum interface? If yes, are solvation energies considered in the force filed development for this organic molecule (that can make the difference) An example of where we observed

Re: [gmx-users] Surface tension calculation for organic monolayer

Dear Spoel, Thanks for your respond. For this simulations I used acids however I got the similar results when I used alcohol (pK values are lower than acids). I doubt this error coming from the pH effects. But how could i get the protonated molecules configuration? > On 07 Jul 2016, at 17:11,

Re: [gmx-users] Surface tension calculation for organic monolayer

On 07/07/16 16:06, gozde ergin wrote: Dear users, I simulated three different systems in cubic box and calculated their surface tension as shown below; 1. Pure water , surface tension = 61.5 mN/m 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m 3.Water surface covered with cis-pinonic

[gmx-users] Surface tension calculation for organic monolayer

Dear users, I simulated three different systems in cubic box and calculated their surface tension as shown below; 1. Pure water , surface tension = 61.5 mN/m 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m 3.Water surface covered with cis-pinonic organic, surface tension = 63.5 mN/m

Re: [gmx-users] Surface tension calculation and counting number of interfacial molecules

Actually you can check both density and surface tension values to understand if it is bulk or interface. To calculate the surface tension as a function of Z, I can suggest you to use Gromacs_LP gromacs source code (which you can download from