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
In the following, the two structures are conformers of alanineglycine that differ by a rotation of the carboxyl group:
20
C 2.081440 0.615100 -0.508430
C 2.742230 1.824030 -1.200820
N 4.117790 1.799870 -1.190410
C 4.943570 2.827040 -1.822060
C 6.440080 2.569360 -1.637600
O 7.351600 3.252270 -2.069090
N 0.610100 0.695090 -0.538780
O 2.095560 2.724940 -1.739670
O 6.705220 1.463410 -0.897460
H 0.303080 1.426060 0.103770
H 0.338420 1.050680 -1.460480
C 2.488753 -0.593400 -1.198448
H 2.416500 0.557400 0.532050
H 4.614100 1.081980 -0.670550
H 4.699850 3.794460 -1.373720
H 4.722890 2.844690 -2.894180
H 7.687400 1.448620 -0.860340
H 2.029201 -1.457008 -0.719999
H 2.170233 -0.542411 -2.238576
H 3.572730 -0.688405 -1.154998
20
C 2.081440 0.615100 -0.508430
C 2.742230 1.824030 -1.200820
N 4.117790 1.799870 -1.190410
C 4.943570 2.827040 -1.822060
C 6.440080 2.569360 -1.637600
O 7.192128 3.169549 -0.890864
N 0.610100 0.695090 -0.538780
O 2.095560 2.724940 -1.739670
O 6.904976 1.547802 -2.400176
H 0.303080 1.426060 0.103770
H 0.338420 1.050680 -1.460480
C 2.488753 -0.593400 -1.198448
H 2.416500 0.557400 0.532050
H 4.614100 1.081980 -0.670550
H 4.699850 3.794460 -1.373720
H 4.722890 2.844690 -2.894180
H 7.856649 1.502460 -2.158231
H 2.029201 -1.457008 -0.719999
H 2.170233 -0.542411 -2.238576
H 3.572730 -0.688405 -1.154998
which produces the outcome
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║ ║
║ ██████╗██████╗ ███████╗███████╗████████╗ ║
║ ██╔════╝██╔══██╗██╔════╝██╔════╝╚══██╔══╝ ║
║ ██║ ██████╔╝█████╗ ███████╗ ██║ ║
║ ██║ ██╔══██╗██╔══╝ ╚════██║ ██║ ║
║ ╚██████╗██║ ██║███████╗███████║ ██║ ║
║ ╚═════╝╚═╝ ╚═╝╚══════╝╚══════╝ ╚═╝ ║
║ ║
║ Conformer-Rotamer Ensemble Sampling Tool ║
║ based on the xTB methods ║
║ ║
╚════════════════════════════════════════════════╝
Version 3.1.0, Thu, 16 July 12:19:58, 07/16/2026
commit (97f4fb8) compiled by 'usr@stellaris'
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.
• P.Pracht, S.Grimme, C.Bannwarth, F.Bohle, S.Ehlert,
G.Feldmann, J.Gorges, M.Müller, T.Neudecker, C.Plett,
S.Spicher, P.Steinbach, P.Wesołowski, F.Zeller,
J. Chem. Phys., 2024, 160, 114110.
for works involving QCG cite
• S.Spicher, C.Plett, P.Pracht, A.Hansen, S.Grimme,
JCTC, 2022, 18 (5), 3174-3189.
• C.Plett, S. Grimme,
Angew. Chem. Int. Ed. 2023, 62, e202214477.
for works involving MECP screening cite
• P.Pracht, C.Bannwarth, JCTC, 2022, 18 (10), 6370-6385.
for works involving the TTConf reimplementaiton cite
• C.Zurek, et al., JCTC, 2025, 21, 1459-1475.
Original code
P.Pracht, S.Grimme, Universität Bonn, MCTC
with help from (alphabetical order):
C.Bannwarth, F.Bohle, S.Ehlert, G.Feldmann, J.Gorges,
S.Grimme, C.Plett, P.Pracht, L.Rindt, S.Spicher,
P.Steinbach, P.Wesolowski, F.Zeller
Online documentation is available at
https://crest-lab.github.io/crest-docs/
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. See the
GNU Lesser General Public License (LGPL) for more details.
Command line input:
$ crest --rmsd struc1.xyz struc2.xyz
> All CLI arguments successfully processed.
> Setting up backup calculator ... done.
> Reading files struc1.xyz and struc2.xyz
Calculated RMSD (Å): 0.48518876
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