[gmx-users] Surface Tension Calculation
dan.gil9973 at gmail.com
Tue Aug 29 18:39:02 CEST 2017
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 sound like a good idea if you are trying to calculate
the surface tension from equilibrium states. Here is a quote from the
online gromacs manual:
> Non-equilibrium MDnon-equilibrium MD*freezegrps:*Groups that are to be
> frozen (i.e. their X, Y, and/or Z position will not be updated; e.g. Lipid
> SOL). *freezedim* specifies for which dimension the freezing applies. To
> avoid spurious contibrutions to the virial and pressure due to large forces
> between completely frozen atoms you need to use energy group exclusions
> <http://manual.gromacs.org/online/mdp_opt.html#egexcl>, this also saves
> computing time. Note that coordinates of frozen atoms are not scaled by
> pressure-coupling algorithms.
In essence, you have to be very knowledgeable about what you are doing.
First of all, this section is under non-equilibrium MD so it already seems
like a bad idea. Freezing the solid phase seems like a bad idea because it
will affect how the solid lattice responds to pressure changes. If you
really know what you are doing, perhaps you can use energy group exclusions
as the manual suggests. But I think that if you have a good force-field for
the solid phase it should be stable even without freezing. Have you tried
simulating without freeze? After careful equilibration and then a
sufficiently long production run, what result do you get for the
interfacial tension from gmx energy?
3. I don't yet see why anything like position restraints or freeze is
On Mon, Aug 28, 2017 at 4:39 PM, Lei <xiaoainisa at gmail.com> wrote:
> 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 and phase 2. I
> followed the typical procedure to calculate the surface tension: phase 1 is
> sandwiched by phase 2 and the interface is planar.
> So my questions are:
> 1. Is there a way to calculate the interfacial tension between phase 1 and
> phase 2?
> 2. Does the freeze command affect the calculation of tension? Do I need to
> freeze phase 1 atoms in the simulation to calculate the interfacial tension
> between phase 1 and phase 2?
> 3. What if I applied the position restraints on the phase 1 atoms instead
> of freezing them?
> Thank you all and enjoy simulating.
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