GSM on hoffman2

Reference:

wiki from the developer (https://github.com/ZimmermanGroup/molecularGSM/wiki)

Tiptorial form Tyler Benton (On Hof2: /u/project/houk/tylerben/shared/GSM/readme.txt)

Tutorial from the Zimmerman Group (https://sites.lsa.umich.edu/zimmerman-lab/tutorial/surface-growing-string-method/)

Personal notes on using GSM with different software on hoffman2.

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Create Working Directory

copy the reference directory to make a new one

cp /u/project/houk/tylerben/shared/GSM/xxxx_GSM/template ./[project_name]

GSM with Gaussian

File setting

gstart - set gaussian input route line // Need the Force keyword

ggrad - Only need to be sure the script is specifying the correct G16 path.

inpfileq - The setting for gsm
The only 3 that may need to changes

• TS_FINAL_TYPE
  • 0 for rotation / 1 for bond change
• NNODES
  • Max number of nodes used for GSM.
  • odd number from 9-15 for DE-GSM
  • higher value to fit more complicated PES
• SM_TYPES
  • Select SSM/GSM/FSM

If use job queue
.cmd - job submission script

• job/out name
• core/memory

Run the job

• Put the input geometry in initial0001.xyz with 2 structures in a row.
• mkdir scratch and place initial0001.xyz under the ./scratch/
• chmod +x gsm.gaussian

Use qrsh

• run qrsh to land on the node
• load module load gaussian
• Use export OMP_NUM_THREADS=# to set the cores GSM main program uses.
• run the job with ./gsm.gaussian 1 1 >> test.log 2>&1 &
  • the first number is for specifying the initial000# file.
  • the second number is for ncpu value in Gaussian input. (for xtb: The in total cpu uses are “ncpu * OMP_NUM_THREADS”. Not sure what it is in gaussian. I tried to set them both into 24 and request a 24 core node. It seems just using 24 cores.

Use submission script

source .bashrc and put the above command used on the compt node in the script.

Restart a job

https://sites.lsa.umich.edu/zimmerman-lab/tutorial/surface-growing-string-method/restarting-growing-string-calculation/

• rename stringfile.xyz#### to restart.xyz#### (same number)
• In inpfileq: change RESTART to 1

(somehow if stringfile.xyz#### hasn’t pop up yet, just resubmit the job would work.)

Aborted with core* files and says chk file is empty
The program misjudge the bond pair. Most likely confused by the leaving group.

Installation

https://github.com/ZimmermanGroup/molecularGSM

• Load cmake > 3.17.0

BTW, is it nessessary to build a new one in a new server?

Misc

• Energy unit is kcal/mol. more
• It seems the original GSM is not in active maintance. Instead they are more active on the pyGSM now.