GaMD-Amber: Installation

LiGaMD in Amber20

LiGaMD has been fully supported in AMBER20, which was released in May 2020 and can be obtained at the Amber website. Instructions for installing the AMBER package can be found in the AMBER manual.

GaMD in Amber16+

GaMD has been fully supported in AMBER16+ since AMBER16 was released on Apr 30, 2016.

GaMD patch for Amber14

“amber14_GaMD_patch_confidential.txt”:
GaMD patch for Amber 14 + AmberTools 15
Authors: Yinglong Miao & Ross C. Walker
Date: 29th July 2015
Programs: pmemd and pmemd.cuda
Description: This patch adds temporary GaMD support to AMBER 14.
It is built against AMBER 14 + AmberTools 15 + Amber 14 updates to 12.
This patch is provided for convenience prior to AMBER 16 release which
will feature GaMD support. It is made available by request only and subject
to your agreement not to redistribute this patch or to provide access to
a GaMD patched copy of AMBER without the written permission of
Ross C. Walker or Yinglong Miao.

By applying this patch you accept these terms and certify that you have
been granted permission to use this with Amber 14 + AmberTools 15.

Suppose you have installed “AMBER 14 + AmberTools 15” (Amber website).
You can apply the GaMD patch and compile the code as the following:

# Uncompress the patch
tar -xvzf amber14-gamd-patch.tgz

# Apply the GaMD patch
# export AMBERHOME to your amber home directory
cp -v amber14_GaMD_patch_confidential.txt $AMBERHOME
cd $AMBERHOME
./update_amber –update
patch -p0 < amber14_GaMD_patch_confidential.txt

# Re-compile the AMBER code
cd $AMBERHOME
./configure gnu
cd $AMBERHOME/src/pmemd/src
make install

cd $AMBERHOME
./configure -cuda gnu
cd $AMBERHOME/src/pmemd/src
make cuda