I am very new in the field of MD Simulations. I have started with a simulation of clay in water (Dynamics of carbohydrate strands in water and interactions with clay minerals: influence of pH, surface chemistry, and electrolytes - Nanoscale (RSC Publishing)). I am using the montmorillonite_CEC90 structure and given force field from supplementary material.
I don’t know how to convert .car/.mdf to .pdb/.psf and then convert the forcefield to gromacs.
I have tried the following command but it’s too many forcefield/automass options applied to one input file (don’t know how to fix this)
$ ./msi2namd.exe -f montmorillonite_CEC90_pH3.car montmorillonite_CEC90_pH3.mdf -res -inp -o montmorillonite_CEC90_pH3.pdb montmorillonite_CEC90_pH3.psf -ignore -nocenter -print 3
Can anyone help me how to solve this problem?
My apologies if it may sounds obvious solution to some people but I am new trying to use this conversion and I am really stuck.
Thank you in advance.