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Leela S. Dodda leelasd

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load ionplte1
sel lig,resname UNK
sel bb, !lig
select SP, bb w. 2.5 of resname UNK
select CSP, br. SP
color iron,lig
show sticks,lig
show sticks,CSP
show spheres, lig
set sphere_scale=0.5,lig
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
leelasd / em.mdp
Created June 16, 2015 05:58
Energy Minimisation Gromacs
; Define
define = -DFLEXIBLE
; Run Control
integrator = steep
; Energy Minimization
emtol = 200.0
nsteps = 5000
@leelasd
leelasd / nvt.mdp
Created June 16, 2015 06:05
Equilibration of Box in NVT ensemble
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.002
nsteps = 5000000
; OUTPUT CONTROL OPTIONS
nstxout = 500
nstvout = 500
nstenergy = 500
nstlog = 500
@leelasd
leelasd / npt.mdp
Created June 16, 2015 06:06
Equilibration of Box in NPT ensemble
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.002
nsteps = 5000000
; OUTPUT CONTROL OPTIONS
nstxout = 500
nstvout = 500
nstenergy = 500
nstlog = 500
@leelasd
leelasd / md_prod.mdp
Created June 16, 2015 06:18
Production run with NPT ensemble
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.002
nsteps = 5000000
; OUTPUT CONTROL OPTIONS
nstxout = 1000
nstvout = 1000
nstenergy = 1000
nstlog = 1000
@leelasd
leelasd / job_gromacs.sh
Created June 16, 2015 06:22
LSF script for running Gromacs in Grace
#!/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
leelasd / dipole_moments_mdtraj.py
Created June 19, 2015 16:01
Static Dielectric Constant from MD_Traj
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
leelasd / EM.mdp
Created June 28, 2015 03:58
G_hyd using FEP with Gromacs
; 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
leelasd / NVT.mdp
Created June 28, 2015 03:59
G_hyd using FEP with Gromacs
; 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 =