GROMACS version: 2018.1
GROMACS modification: No
Hi everyone, in one of my MD simulations with a small molecule in water, gmx sasa results in the atom’s SASA to be always a multiple of 0.038 (0, 0.038, 0.075, 0.0113). The SASA of the atom always takes one of these discrete values for the entire MD simulation. I noticed the same thing for another atom of that small molecule.
Is this an indication that I am running the sasa command wrong? The options I use are -surface ‘small molecule’ -output ‘atom of small molecule’
Hi,
If you want to calculate the accessible solvent surface of a molecule in solution and output the atom information you can run gmx sasa with option -ao.
I recalled that you post a similar question before. But I could not understand why you use -surface.
Best regards
Alessandra
Thank you Alessandra! I decided to repost my question in an abbreviated form in case my first post was not easy to understand…
The -oa option provides only the average and standard deviation. With the options I am using, I get the SASA over time which I can then analyze and get the frequency distribution (which is what I wanted to do).
I do not know why the atomic SASA takes only discrete values during my 1.5 us simulation.
The -oa option does work fine but it provides only an average…
There are only going to be so many grid points on the surface that can be assigned to any atom, so if you’re just computing the SASA of a single atom, it seems quite likely to only assume discrete values. You can see if it varies by increasing the value of -ndots when executing gmx sasa. If it does, you have your answer, but I think this is likely it.
That took care of it, thank you Justin.