leelasd

This post examines the features of [R Markdown](http://www.rstudio.org/docs/authoring/using_markdown) 
using [knitr](http://yihui.name/knitr/) in Rstudio 0.96.
This combination of tools provides an exciting improvement in usability for 
[reproducible analysis](http://stats.stackexchange.com/a/15006/183).
Specifically, this post 
(1) discusses getting started with R Markdown and `knitr` in  Rstudio 0.96;
(2) provides a basic example of producing console output and plots using R Markdown;
(3) highlights several code chunk options such as caching and controlling how input and output is displayed;
(4) demonstrates use of standard Markdown notation as well as the extended features of formulas and tables; and 
(5) discusses the implications of R Markdown.

leelasd

; Define
define		= -DFLEXIBLE

; Run Control
integrator	= steep

; Energy Minimization
emtol		= 200.0
nsteps		= 5000

leelasd

; RUN CONTROL PARAMETERS
integrator	= md
dt		= 0.002
nsteps		= 5000000

; OUTPUT CONTROL OPTIONS
nstxout		= 500
nstvout		= 500
nstenergy	= 500
nstlog		= 500

leelasd

; RUN CONTROL PARAMETERS
integrator	= md
dt		= 0.002
nsteps		= 5000000

; OUTPUT CONTROL OPTIONS
nstxout		= 500
nstvout		= 500
nstenergy	= 500
nstlog		= 500

leelasd

; RUN CONTROL PARAMETERS
integrator	= md
dt		= 0.002
nsteps		= 5000000

; OUTPUT CONTROL OPTIONS
nstxout		= 1000
nstvout		= 1000
nstenergy	= 1000
nstlog		= 1000

leelasd

#!/bin/bash
#BSUB -o .                       ## requests outfile be generated
#BSUB -a openmpi
#BSUB -q shared                  ## specify queue to run on, shared = default
#BSUB -J FAM           ## job-name
#BSUB -W 24:00                   ## walltime <HH:MM>= 24 hrs
#BSUB -n 4  
#BSUB -R "rusage[mem=50000]"     ## memory limit= MB count only (1024MB = 1GB)
module load Apps/Gromacs 
grompp -f em.mdp -c 267_fam_box.gro -p 267_fam_box.top -o em.tpr

leelasd

import numpy as np
import mdtraj as md
from mdtraj.geometry.thermodynamic_properties import *
import mdtraj.utils.unit.unit_definitions as u

temperature=300
traj = md.load('md_prod2.xtc', top='md_prod2.gro')
charge=np.genfromtxt('charges',dtype='f8',usecols=[0])
charges=np.tile(charge,267)
print static_dielectric(traj, charges, temperature)

leelasd

; RUN CONTROL PARAMETERS = 
integrator               = steep
; start time and timestep in ps = 

; 6 ns.  This turns out to be long enough for systems without slow intramolecular degrees of freedom
nsteps               = 5000
emtol 		     = 100
emstep		     = 0.01	
; mode for center of mass motion removal = 

leelasd

; RUN CONTROL PARAMETERS = 
integrator               = sd
; start time and timestep in ps = 
tinit                    = 0
dt                       = 0.002

; 1 ns.  This turns out to be long enough for systems without slow intramolecular degrees of freedom
nsteps               =  500000
; mode for center of mass motion removal = 

leelasd

; RUN CONTROL PARAMETERS = 
integrator               = sd
; start time and timestep in ps = 
tinit                    = 0
dt                       = 0.002

; 6 ns.  This turns out to be long enough for systems without slow intramolecular degrees of freedom
nsteps               = 1000000
; mode for center of mass motion removal =