Subject: [bug#40691] [PATCH] gnu: Add gromacs.

From: Vincent Legoll <[email-masked]>
Date: Sat, 18 Apr 2020 00:24:44 +0200

* gnu/packages/bioinformatics.scm (gromacs): New variable.
---
 gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b9be0c1918..f0fca30dd8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17,6 +17,7 @@
 ;;; Copyright © 2019 Brett Gilio <[email-masked]>
 ;;; Copyright © 2020 Björn Höfling <[email-masked]>
 ;;; Copyright © 2020 Jakub Kądziołka <[email-masked]>
+;;; Copyright © 2020 Vincent Legoll <[email-masked]>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -785,6 +786,44 @@ input/output delimiter.  When the new functionality is not used, bioawk is
 intended to behave exactly the same as the original BWK awk.")
     (license license:x11)))
 
+(define-public gromacs
+  (package
+    (name "gromacs")
+    (version "2020.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1kwrk3i1dxp8abhqqsl049lh361n4910h0415g052f8shdc6arp1"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list "-DGMX_DEVELOPER_BUILD=on")))
+    (native-inputs
+     `(("doxygen" ,doxygen) ; need dot
+       ("python-sphinx" ,python-sphinx))) ; problem reported by cmake
+    (inputs
+     `(("fftwf" ,fftwf)
+       ("hwloc" ,hwloc-2 "lib")
+       ("imagemagick" ,imagemagick)
+       ("lapack" ,lapack)
+       ("openblas" ,openblas)
+       ("openmpi" ,openmpi)
+       ("perl" ,perl)))
+    (home-page "http://www.gromacs.org/")
+    (synopsis "Molecular dynamics software package")
+    (description "GROMACS is a versatile package to perform molecular dynamics,
+i.e. simulate the Newtonian equations of motion for systems with hundreds to
+millions of particles.  It is primarily designed for biochemical molecules like
+proteins, lipids and nucleic acids that have a lot of complicated bonded
+interactions, but since GROMACS is extremely fast at calculating the nonbonded
+interactions (that usually dominate simulations) many groups are also using it
+for research on non-biological systems, e.g. polymers.  GROMACS supports all the
+usual algorithms you expect from a modern molecular dynamics implementation.")
+    (license license:lgpl2.1+)))
+
 (define-public python-pybedtools
   (package
     (name "python-pybedtools")
-- 
2.26.0