Statistical Analysis Method for Peak force and total work in Steered molecular dynamics

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Is a two-sample t-test reasonable for comparing SMD results between groups?

If not T-test then what other statistical method would be appropriate and why?

I have four groups (protein-protein), 10 replicates for each protein-protein group. I want to plot the graph and perform statistical analysis for peak force and total work across 4 groups.

To create the replicates within each SMD group, I used

  • Same pressure-equilibrated .gro starting structure

  • Different velocity seeds for each replicate

  • Same pulling protocol for all groups

Would you treat the replicates within each group as an independent enough for pairwise t-tests?

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A few checks before applying a t-test:

Do the peaks (max force value in each simulation) assume a normal distribution in your 4 systems?

Are you equilibrating every replica briefly before starting the pulling so that the pulling is not starting from exactly the same coordinates?

3

Thank you for your response.

Each SMD replicate was initiated using different velocity seeds from the same pressure-equilibrated starting structure(.gro) under identical pulling conditions.

Does this make the replicates partially dependent? If so, how can I make them truly independent or given my simulation conditions, what other statistical test would be more appropriate? I am so confuse on the correct approach in my case.

Also the smd code for velocity generation that I used is this:



gen_vel         = yes        
gen_temp        = 310       ; temperature for Maxwell distribution
gen_seed        = 102        ; generate a random seed, for replication 2

I am not assuming normal distribution for force. Rather my force profile look like this- multimodal distribution. But this distribution does has a biological reason.

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