Multiwfn is the best program to carry out NCI analysis, I don't believe there is any reason to use other codes. Multiwfn is much faster, more powerful, more flexible and easier to use. There have been about 1000 published papers that have successfully used Multiwfn to realize NCI analysis. Please check Section 3.23.1 of Multiwfn manual, which very clearly and detailedly illustrates how to perform NCI analysis. .fchk file can be directly used as input file for NCI analysis purpose.

Section 5.2 and 5.3 described how to run Multiwfn in silent mode and write shell script to automate the analysis, therefore you can very easily perform NCI analysis for a large batch of systems.

I am going through several .fchk files needed to convert in .wfn file format to run in NCIPLOT. In the Multiwfn d3.6 manual Icould understand the procedure to convert several .fchk file to .wfn file format. I am looking for a linux script that could help me. I am new to linux so please if anybody can help me there.