Should I do repeats of my systems for validity

User discussions
1

GROMACS version: 2020.2
GROMACS modification: No
I’m conducting simulations of multiple peptide systems interacting with a model bacterial bilayer, I wonder if it’s necessary to conduct repeat simulations with different starting velocities so my particles will move on different trajectories in order to add validity to my results? Is one simulation enough? I can’t tell from reading papers if other people do this :) (These are coarse-grained 3-5us simulations so they do take a while to run and analyse)

Thanks in advance!

Anna

2

Replicates are standard practice in all MD work. Otherwise, you have no idea if your observation is the statistical outlier or the normal behavior (almost every paper you read should report replicates).

For association/complexation processes, I think it is inadequate to simply start with different velocities and the same coordinates. You should start from alternate configurations to see if the same assembly properties are observed.

3

Thanks for responding!

If I have a fixed number of peptides interacting with a model bilayer, by changing their orientation along their axes to random for each peptide, would this be an alternate configuration?

Currently, the peptide starting locations are fixed (They all fit nicely above the bilayer 0.3 - 0.5 nm apart in a grid-like format to sit above the bilayer in the given space) but I’m not sure how I would vary this arrangement to make them sufficient alternate configurations?

Thanks again!

Anna

4

Altering the coordinates to produce different initial configurations should be adequate.

5

Okay great thank you! Do you know a suitable way of inserting molecules randomly, a certain distance apart along one plane in the z direction? I have been using a pos.dat file where I suggest the coordinates to place the molecules but I wonder if there is a way to make it completely randomised each time? I have tried the insert-molecules command: gmx insert-molecules -f my_bilayer.gro -ci peptide.gro -box 13 13 1 -try 500 -radius 0.5 -o trying_something_new.gro -nmol 24, but I can’t seem to get them to be placed flat along one axis.

Thanks!

Anna

6

You can try gmx genconf -rot but that will probably rotate in all dimensions so I don’t know if it’s what you want. Otherwise, the pos.dat approach is appropriate and you could apply random rotations to different molecules with gmx editconf.

7

Thanks so much this has helped loads!

I’ve made a slightly larger system so I can move all peptides around more freely for independent repeats!

Thanks so much!

Anna