Calculating RMSDs

How to calculate a Cartesian RMSD with CREST.

Calculating Cartesian RMSDs

The calculation of Cartesian RMSDs as a standalone tool in CREST is straight-forward with the --rmsd <FILE1> <FILE2> option. Assuming the two structures to be compared are named struc1.xyz and struc2.xyz, the CREST command would be

crest --rmsd struc1.xyz struc2.xyz

which produces the outcome

       ==============================================
       |                                            |
       |                 C R E S T                  |
       |                                            |
       |  Conformer-Rotamer Ensemble Sampling Tool  |
       |          based on the GFN methods          |
       |             P.Pracht, S.Grimme             |
       |          Universitaet Bonn, MCTC           |
       ==============================================
       Version 2.12,   Thu 19. Mai 16:32:32 CEST 2022
  Using the xTB program. Compatible with xTB version 6.4.0
 
   Cite work conducted with this code as

   • P.Pracht, F.Bohle, S.Grimme, PCCP, 2020, 22, 7169-7192.
   • S.Grimme, JCTC, 2019, 15, 2847-2862.

   and for works involving QCG as

   • S.Spicher, C.Plett, P.Pracht, A.Hansen, S.Grimme,
     JCTC, 2022, 18 (5), 3174-3189.
 
   with help from:
   C.Bannwarth, F.Bohle, S.Ehlert, S.Grimme,
   C.Plett, P.Pracht, S.Spicher
 
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

 Command line input:
 > crest --rmsd struc1.xyz struc2.xyz

 Calculated RMSD (Å):      1.48259461

The RMSD will always be printed in Å, regardless of the input file format of <FILE1> and <FILE2>. Since the RMSD is printed as the last line of this CREST printout, it can easily be read from the command line (e.g. for scripting purposes)

crest --rmsd struc1.xyz struc2.xyz | tail -1