6.1. Input File for geom

The input file for geom is completely different from other components. Below is an example that contains all options available in geom.

Tip

If you hate reading this lengthy introduction, you can simply copy this input file and just change the items you need for your research.

geom.inp

lm_dir          mol      # Save the local minima to this folder.
num_calcs       1000     # Total number of calculations.
do_coarse_opt   yes      # no: Do NOT the coarse optimization.
min_energy_gap  1.E-4    # When two energies differ smaller than
                         # this value, they are treated as identical.
                         # A negative number means do not remove
                         # energetically degenerated ones.
max_geom_iters  3000     # The maximum number of iterations for local optimization.
                         # If it is less or equal than zero, then the number is unlimited.

components
  water.xyz 1000
  box 0 0 0 30 30 30
  ****
  xylitol.xyz 1000
  fix 0 0 0 15 15 15
  nH nH
  ****
end

charmm # Parameters and PSF.
  test/par_all35_ethers.prm
  test/ether.psf
end

xtb # charge, uhf, gfn, (solvent)
  0 0 2
end

savegjf
  %chk=gsh-$index$.chk
  %mem=10GB
  %nproc=24
  $hash$MP2/cc-pVTZ Opt Freq Output=wfn
  $blank$
  GSH generated from ABCluster, energy = $energy$
  $blank$
  0 1
  >>>>
  gsh-$index$.wfn
end

commands
  $charmm$
end

• Statements after # are comments. You can also put blank lines anywhere.

• Line 1: lm_dir is the path to save local minima. Here the path is mol.

• Line 2: num_calcs is the number of calculations, i.e. \(g_\text{max}\). Here it is 1000.

• Line 3: do_coarse_opt suggests if a coarse optimization is done before submitting the structure. We strongly recommend that this is set to yes.

• Line 4: min_energy_gap is the minimum energy gap that two structure are treated as identical. In this case is 1E-4. This means, if geom predicts two clusters of energy -1.00054 and -1.00051, their energy gap is then 0.00003 < 1E-4, so the two structure will be treated as the same: one of them will be discarded.

• Line 8: max_geom_iters is the maximum number of iterations for local optimizations. Here is 3000. For example, geom internally-integrated xTB and CHARMM will do local optimization no more than 3000 steps.

• Line 11 to 19: components controls the cluster component and shape. It will be discussed in details in Control the Cluster Shape.

• Line 21 to 24: charmm gives the CHARMM force field parameter file (only 1) and PSF files for each component, if internally-integrated CHARMM is called. Also, geom will save a PDB file for each optimized cluster. This input block (Line 21 to 24) can be deleted if you do not need CHARMM calculation or PDB output.

• Line 26 to 28: xtb gives options to call internally-integrated xTB. It can be 3 integers, corresponding to the three options of xTB:

Reserved words	Meaning
--chrg	The charge of the whole cluster.
--uhf	The number of unpaired electrons.
--gfn	The Hamiltonian type, being 0, 1, 2 or , 3 (GFN-FF).

It can also be 3 integers plus a solvent, then analytical linearized Poisson-Boltzmann implicit solvation model will be turned on in xTB engine. Available solvents are:

Solvent
Acetone
Acetonitrile
Aniline
Benzaldehyde
Benzene
CH2Cl2
CHCl3
CS2
Dioxane
DMF
DMSO
Ether
Ethylacetate
Furane
Hexadecane
Hexane
Nitromethane
Octanol
Phenol
Toluene
THF
H2O

• Line 30 to 41: savegjf gives options to save the optimized clusters in Gaussian input format. It is very similar to optfile introduced in isomer with Gaussian: the things before and after >>>> will be put before and after the coordinates. This input block (Line 30 to 41) can be deleted if you do not need GJF output. There are 4 “reserved words” to use here:

Reserved words	Meaning
$hash$	The hashtag #.
$blank$	A blank line.
$index$	The index of this structure like 3.
$energy$	The optimized energy of this cluster.

• Line 43 to 45: commands tells geom how to call internally-integral or third-party computational chemical modules. While this is completely the same as introduced in Interfaces to External Programs, there are three additional powerful functions:

Reserved words	Meaning
Empty	geom will generate reasonable structures by itself.
$xTB$	Internally-integrated xTB will be called to do local optimization.
$charmm$	Internally-integrated CHARMM will be called to do local optimization.

We will introduce geom in details in the following.

6.2. Restart or Continuation

From ABCluster 3.1, calculations with geom can be restarted or continued.

For example, assume you do a calculation with the input file geom.inp above, you have asked for 1000. If the calculation was interrupted for some reasons at 498, you just need to call geom geom.inp again. As long as the directory mol is not destroyed, geom will restart the calculation from 498 automatically.

Or, assume you want to do extra 500 steps after the above job normally terminates, just change num_calcs 1000 to num_calcs 1500. As long as the directory mol is not destroyed, geom will restart the calculation from 1000 automatically.

Attention

For a meaningful restart or continuation, do NOT change anything in the input file except num_calcs.