How to run pyGSM

[ms860309]

I think it's easily to use pyGSM. Here's a introduction You may also use the following guide.

1. Install the calculator. I recommend you to use xTB for your first run.

   conda activate gsm_env
   conda install -c conda-forge xtb-python

2. Prepare your input file. Maybe you can use this ./data/diels_alder.xyz for the double ended gsm.
3. Run gsm

   export MKL_NUM_THREADS=1
   export OMP_NUM_THREADS=1
   export OMP_STACKSIZE=1G
   gsm -xyzfile ./data/diels_alder.xyz -mode DE_GSM -package xTB_lot > status.log 2>&1

[shaoqx]

How do you configure the level of theory used in xtb? Will there be a lot_inp_file? Thanks

[RaphaelRobidas]

In addition to -package xTB_lot, you can use the -xTB_Hamiltonian option, which allows you to select GFN2-xTB or GFN1-xTB.

[shaoqx]

Cool! Thank you! Just found that also from gsm --help. Also I found the nnodes flag from the examples does not work and I think now gsm use -num_nodes to specify this. Also I want to ask if there any option that correponding to the original TS_FINAL_TYPE and BOND_FRAGMENTS

Also would you mind explain a little bit about multithreading? I found there are multiple ways to specify that:

MKL_NUM_THREADS
OMP_NUM_THREADS

and the -nproc flag. What are the differences? Thanks!