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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 |
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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. |
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; Define | |
define = -DFLEXIBLE | |
; Run Control | |
integrator = steep | |
; Energy Minimization | |
emtol = 200.0 | |
nsteps = 5000 |
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; RUN CONTROL PARAMETERS | |
integrator = md | |
dt = 0.002 | |
nsteps = 5000000 | |
; OUTPUT CONTROL OPTIONS | |
nstxout = 500 | |
nstvout = 500 | |
nstenergy = 500 | |
nstlog = 500 |
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; RUN CONTROL PARAMETERS | |
integrator = md | |
dt = 0.002 | |
nsteps = 5000000 | |
; OUTPUT CONTROL OPTIONS | |
nstxout = 500 | |
nstvout = 500 | |
nstenergy = 500 | |
nstlog = 500 |
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; RUN CONTROL PARAMETERS | |
integrator = md | |
dt = 0.002 | |
nsteps = 5000000 | |
; OUTPUT CONTROL OPTIONS | |
nstxout = 1000 | |
nstvout = 1000 | |
nstenergy = 1000 | |
nstlog = 1000 |
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#!/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 |
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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) |
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; 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 = |
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; 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 = |
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