Halo experts
I have found force autocorrelation function for few of windows generating for drug pull from aqueous to lipid bilayer centre as negative. Is it correct? What is the meaning of negative force autocorrelation function . And so diffusion coeffients calculated from this values are also negative. Is it correct?
Please help
A negative diffusion coefficient indicates that something is not correct. Could you post a plot of the autocorrelation function, and also the options you used when generating it? What pull-nstfout did you use? Or rather, what was the time interval between the force outputs?
Respected Sir
Here I present my mdp files from pulling to npt equilibration for one window and 2 screenshots.
- direction-periodic pulling
direction.mdp (2.3 KB) - nvt for 300 ps , direction pulling setup
step6.1_equilibration.mdp (1.9 KB) - npt for 30ns, direction pulling setup
step6.3_equilibration.mdp (2.1 KB) - pullf plot after npt
- gromacs output reading for force autocorrelation obtained from immediate above.
Thank you for your kind cooperation
Goodday!
I would also like to mention that the drug molecule after pulling as well as after npt equilibration tend to end up in edges of the box . I present here screenshots of it.
- After pulling
- After npt equilibration
I’m not sure what you want to achieve with your force autocorrelation functions. You said above that you “found force autocorrelation function for few of windows”, so I assumed you were doing umbrella sampling simulations. But in the mdp (direction.mdp) you are using directional pulling rates. I don’t think you can calculate diffusion coefficients from that, at least I don’t know how to do it.
This is the equation I am using to calculate perpendicular diffusion of drug molecule to the lipid bilayer centre for each window.
But you are pulling directionally. The umbrella sampling windows should be still.