GROMACS version: 2020
GROMACS modification: No
Hi
I am trying to use the combination of gmx covar and gmx anaeig with the -entropy flag to calculate entropies for model peptides. The output I recover is a simple number for each of the methods available. I would need the time evolution of the value, in order to check whether the calculation is converging. Is there an option available to recapitulate that result?
Thanks,
David
To get the evolution of your entropy you need to calculate it cumulatively, depending on your simulation time, let’s say at 2 ns, 4 ns, … and plot it.
Can you please state how to do this cumulatively so that I can plot the data
Easy! You can just write a for loop in your favourite scripting language invoking gmx covar with different (increasing) values of the flag -e. In this way you will include larger amounts of data in each calculation and eventually the estimate of the entropy will converge, provided you have sampled for long enough.