[gmx-users] surface tension in free energy calculation

Dear All, I’m simulating a system of monolayer/water interface and I want to calculate the change in the free energy (using Jarzynski method if possible) of my system in the following process. First, my system box is compressed to a certain size (by moving boundaries) and then it is expanded

[gmx-users] Surface tension calculations via gmx energy?

Dear GROMACS users, Using gmx energy I am trying to compute surface tension for the membrane system in GROMACS under different surface tension. In the model surface tension was modeled by various negative lateral pressure: Pxy surf*surftension 1 bar -33.8847 -10 bar 155.696 -20 bar 240.326 -30

[gmx-users] Surface Tension: equation and tail corrections?

Hello GROMACS users, I am using gromacs 2018.1 The manual and the gmx energy help page does not explicitly explain how the "(surface tension) x (surface number)" is calculated. I assume it is equation 3.69: L_{z} ( P_{zz}(t) - ( 0.5*P_{xx}(t) + 0.5*P_{yy}(t) ) ) Has anyone implemented a tool

[gmx-users] surface tension coupling

Dear Gromacs Users, I want to obtain the surface pressure–area isotherm of a surfactant monolayer at the air–water interface by means of surface tension coupling and make a comparison with the experimental isotherm. Therefore, I generated a gromacs mdp file which is in below and I'm especially

[gmx-users] Surface tension from gmx energy

Dear Gromacs Users! I am interesting how is possible to obtain the value for the surface tension via the output from the gmx energy. E.g. on the example I have two outputs where in the second case the ST were introduced via the adding the negative lateral pressure along XY: # 1) no surface

Re: [gmx-users] Surface tension for water

I cannot understand the point of performing NPT coupling to compute surface tension, the usual approach relies on NVT simulations instead. You might want to take a look at this very nice investigation of the surface tension of many water models (all done using GROMACS at constant NVT conditions):

Re: [gmx-users] Surface tension for water

Dear Dan, As you can see in the images I sent to you, there is no error massage in output files. The properties of the system such as pressure or temperature is so high, that's why I've concluded that the system is crashed. Sincerely, Iman On Wed, Aug 30, 2017 at 12:44 AM, Iman Ahmadabadi <

Re: [gmx-users] Surface tension for water

Iman, You get the error message in the terminal if you are running it on your own machine. If you are running on a supercomputer, the error messages will be directed to a file. How do you know the simulation is crashing without the software telling you? Please find the message (check all

Re: [gmx-users] Surface tension for water

Hi Dan, There is no error massage, It's just a crashing and stopping the simulation. The version is 4.6.0. Iman On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi wrote: > Dear Dan, > > I have attached the NPT.mdp file in the following: > > title = NPT

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 for water

Dear Dan, I have attached the NPT.mdp file in the following: title = NPT equilibration ; Run parameters integrator = md nsteps = 2000 dt= 0.001 ; Output control nstxout = 500 nstvout = 500 nstenergy = 500 nstlog = 500 ; Bond parameters continuation= no constraint_algorithm

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

Re: [gmx-users] Surface tension for water

What is the error message? What version of Gromacs are you using? Can you post the entire .mdp file? On Tue, Aug 29, 2017 at 9:34 AM, Iman Ahmadabadi wrote: > Dear All Users, > > I'm calculating the surface tension of the water, my box contains almost > 5000 water

[gmx-users] Surface tension for water

Dear All Users, I'm calculating the surface tension of the water, my box contains almost 5000 water molecule in the middle of that. Through NVT equilibration, I got reasonable results for surface tension but when I use NPT for my system, the system crashes every time. The pressure coupling

[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

[gmx-users] Surface tension/pressure calculation

Dear all, I would like to calculate surface tension/pressure of my monolayer simulation. I have two monolayers of lipid each side of a water box. So four interfaces; vaccum/lipid, lipid/water, water/lipid and lipid/vaccum. I used NVT simulation. Is there a way to calculate surface

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 coupling with Parrinello-Rahman algorithm

Dear André, In that publication it is specified the use of semi-isotropic pressure coupling, not the surface-tension option in Gromacs. They were controlling the surface tension applying a different pressure in XY than in Z. But I guess it still different from my question, which is related to the

Re: [gmx-users] Surface tension coupling with Parrinello-Rahman algorithm

I'd guess it works since it has been done already: http://www.sciencedirect.com/science/article/pii/S0005273613004501 On Wed, May 25, 2016 at 10:31 AM, Giuseppe Léonardo Licari < giuseppe.lic...@unige.ch> wrote: > Dear all, > I have a question concerning the Surface-Tension pressure coupling in

[gmx-users] Surface tension coupling with Parrinello-Rahman algorithm

Dear all, I have a question concerning the Surface-Tension pressure coupling in NPT simulation of a water/dodecane interface. In the Gromacs 5.1 manual it is reported that the coupling of the surface tension to the XY-plane works only with Berendsen algorithm. I tried to do the MD simulation

Re: [gmx-users] Surface tension

Thank you Andre. Your explanation answers my question very well. On Tue, May 10, 2016 at 10:31 PM, André Farias de Moura wrote: > Hi Ganesh, > > as any other pressure-related property, surface tension values over narrow > timescales are really noisy for systems in the range of

Re: [gmx-users] Surface tension

Hi Ganesh, as any other pressure-related property, surface tension values over narrow timescales are really noisy for systems in the range of nanometers (increasing area should reduce the fluctuation). If simulations last long enough, average values should be OK (please mind that average values

[gmx-users] Surface tension

Dear Gromacs Users, I have been trying to calculate the surface tension of pure water in a cubic box, in which a layer of water molecules (along the XY plane) is surrounded by vacuum on either sides of the Z-direction. Towards this, I did an NVT simulation and computed the surface tension using

[gmx-users] Surface tension: output units

What are the units of surface tension derived thru g_energy? I am confused with the header: (kJ mol\S-1\N) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Surface tension: output units

That is unfortunately a generic unit for energy written by gmx energy without enough sensitivity, and wrong in this case. I believe it's supposed to be bar nm. Mark On Mon, 25 Jan 2016 02:39 VITALY V. CHABAN wrote: > What are the units of surface tension derived thru

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

[gmx-users] Surface tension for membrane simulation

Hi all, I have a question of surface tension in membrane simulation. I found that in equilibration and production step, the pressure set up for membrane simulation is below: ; Pressure coupling is on pcoupl          = Parrinello-Rahman         ; Pressure coupling on in NPT pcoupltype      =