I’m using Drude version of GROMACS 2016 code to study the effect of phosphate ions on surface tension in a biphasic system (tetradecane/water). In this regard, I’d like to perform some analysis, namely:
- Concentration and charge density distribution of ions:
I guess I can use gmx density tool to get the density profile along the z-axis perpendicular
to the interface
- Ion concentration at the interface:
Namely, counting and averaging number of ions entered into a pre-defined interface
- Residence time:
Namely, assessing the rate of ion swapping between bulk and interface regions. Hence, counting the number of ions come into an interface at time t0 and retained until t0+t.
Can you give me so input on these?
Thank you in advance
Concentration and charge density distribution of ion
Yeah, density along the z axis is reasonable here
Ion concentration at the interface
Depending on exactly what you’re looking for, I believe
gmx mindist with the -on output flag will keep a running count of the number of particles within a certain distance of a reference group. You may also need to use the -group option.
This ones a bit trickier. There may be a tool for it but I’m not aware. It may require some programming. You could load your trajectories into a format consumable by python using MdTraj or MdAnalysis (there are other frameworks as well) and do it yourself. You may also be able to shortcut the trajectory loading by getting the per-phosphate distance to your reference data and using that as a starting point for programatic analysis. Probably either
gmx distance or
gmx mindist has per-particle breakdowns as options, but in the worst case you could make a bunch of indexes and run the program on each of them.
Thank you for your input,
I have a biphasic system, water/tetradecane, with phosphate ions on the water side. I’d like to count the number of ions entering in a (-z,+z) region.
The problem with gmx mindist is it makes no use of selection options so that I cannot point out box coordinates.
Ah, in that case check out the various counting options of
gmx select. TBH it may work for your other use cases as well. The selection syntax doc will be helpful