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Wes Barnett, PhD wesbarnett

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View aws.md

Server setup

AWS

  1. Visit https://aws.amazon.com and sign up for an account.
  2. Install and configure the aws-cli program according to here.

Then do:

View gist:aec944bf09bcfbdd2df21509dc3b81ca
make[1]: Entering directory `/rigel/cheme/users/jwb2162/lammps/src/Obj_serial'
make[1]: Leaving directory `/rigel/cheme/users/jwb2162/lammps/src/Obj_serial'
make[1]: Entering directory `/rigel/cheme/users/jwb2162/lammps/src/Obj_serial'
icpc -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLMP_USER_OMP -I../STUBS -c ../npair_full_nsq_omp.cpp
icpc -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLMP_USER_OMP -I../STUBS -c ../reader_xyz.cpp
icpc -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLMP_USER_OMP -I../STUBS -c ../npair_full_bin_atomonly_omp.cpp
icpc -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLMP_USER_OMP -I../STUBS -c ../npair_halffull_newton_omp.cpp
icpc -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLMP_USER_OMP -I../STUBS -c ../fix_dt_reset.cpp
icpc -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLMP_USER_OMP -I../STUBS -c ../fix_nph_sphere_omp.cpp
icpc -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLMP_USER_OMP -I../STUBS -c ../fix_deform.cpp
@wesbarnett
wesbarnett / backup
Created Apr 28, 2016
Incremental backup to external drive using snapper and btrfs send/receive
View backup
#!/bin/bash
# James W. Barnett
# Takes snapshots of each snapper configuration. It then sends the snapshot to
# a location on an external drive. After the initial transfer, it does
# incremental snapshots on later calls. It's important not to delete the
# snapshot created on your system since that will be used to determine the
# difference for the next incremental snapshot.
# Can set the backup directory here, or in the snapper configuration file with
View 41_snapshots-btrfs
#! /usr/bin/bash
#
# This is a fork of Antynea's grub-btrfs, witch changes to make it specific for
# snapper
#################################################################################################################################################
# Written by: Antynea #
# #
# Purpose: Include btrfs snapshots at boot options (grub-menu). #
# #
@wesbarnett
wesbarnett / PKGBUILD
Created Jun 25, 2015
PKGBUILD for GROMACS
View PKGBUILD
pkgname=gromacs
pkgver=5.0.5
pkgrel=1
pkgdesc='A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of
motion for systems with hundreds to millions of particles.'
url='http://www.gromacs.org/'
license=("LGPL")
arch=('i686' 'x86_64')
depends=('fftw-bettersimd')
makedepends=('cmake')
@wesbarnett
wesbarnett / eqlA.mdp
Created Apr 18, 2015
mdp files for free energy of solvation of neopentane
View eqlA.mdp
integrator = sd
dt = 0.002 ; 2 fs
nsteps = 50000 ; 100.0 ps
nstxout = 0
nstvout = 0
nstfout = 0
nstenergy = 500
nstdhdl = 0
separate-dhdl-file = yes
@wesbarnett
wesbarnett / run
Created Apr 15, 2015
Run script for Gromacs free energy calculations
View run
#!/bin/bash
set -e
for ((i=0;i<11;i++)); do
gmx grompp -f minA$i.mdp -po minA$i -pp minA$i -o minA$i
gmx mdrun -deffnm minA$i -v
gmx grompp -f minB$i.mdp -po minB$i -pp minB$i -o minB$i -c minA$i -maxwarn 1
@wesbarnett
wesbarnett / neopentane.top
Created Apr 15, 2015
Neopentane TraPPE-UA topology
View neopentane.top
; Include forcefield parameters
#include "trappeua.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Neopentane 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 NPA rtp NPA q 0.0
View gist:7715c84ef46ca8a2c708
; Include forcefield parameters
#include "trappeua.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Neopentane 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 NPA rtp NPA q 0.0
@wesbarnett
wesbarnett / lambda-script
Created Apr 15, 2015
Script for generating mdp files with different lambda states
View lambda-script
#!/bin/bash
for ((i=0;i<11;i++)); do
sed -e "s/MYLAMBDA/$i/g" minA.mdp > minA$i.mdp
sed -e "s/MYLAMBDA/$i/g" minB.mdp > minB$i.mdp
sed -e "s/MYLAMBDA/$i/g" eqlA.mdp > eqlA$i.mdp
sed -e "s/MYLAMBDA/$i/g" eqlB.mdp > eqlB$i.mdp
sed -e "s/MYLAMBDA/$i/g" prd.mdp > prd$i.mdp
echo $i
done
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