一个人擅长什么，不擅长什么，基本是后天的事情

如果我们承认知识和能力是后天学习而来，那么一个人擅长什么，不擅长什么，完全是后天决定的，也是每天的习惯决定的。

比如一个人不擅长英语写作，如果每天能用一个小时写作200-300字的英文短文，一年之后他就会成为英文写作的专家。当然，要有效的学习。

再比如一个人不擅长编程，如果每天花一个小时编程，一年之后就可以成为C/C++, JAVA的专家。当然，人不能太笨。

比如一个人如果不擅长英文阅读或是听说， 如果每天花一个小时练习听力，阅读或是当众演说，一年之后就可以成为英文读听说的专家。当然，人还是不能太笨。

最后，如果看人不擅长什么，就看他最近一年的工作，在重复做些什么？如果一个编程的人过去一年全在看小说，旅游，我们说这个人暂时废掉了。给一个月还是可能恢复的。当然，你如果从来没有学过英语和编程，大概连废掉的机会都么有。

我个人感觉，每天最理想的是花一个小时学习新东西，可以是新方法，比如编程JAVA的可以学学C/C++。比如做科研的，每天可以花一个小时看看别人用的什么新设备，软件，数值方法，或是新概念，然后动手去试试看。其余7个小时吗，还是老老实实做好自己的老本行。科研写文章，马工找工作，都是懂得越多越有市场，不是吗？

所以说，擅长都是练出来的，擅长都是时间堆出来的。

Conjugation effects, molecular wire and charge transport property

Related note
quantum interference:

Considering wave-particle duality of real world objects, we can conclude any two objects can interfere with each other. And of course, human beings (can be regarded as particles) can interfere with each other too. We can conclude that the wavelength of a person with 60 kg weight is lambda (wavelength) = h/p =6.63/10^(-34) (J.s) / (60(kg)*465.1 m/s) (Speed: the equatorial speed of the earth) = 2.38 * 10 ^(-38) m.

Conjugation effect: a conjugated system is a system of connected p-orbitals with delocalized electrons in compounds with alternating single and multiple bonds, which in general may lower the overall energy of the molecule and increase stability. 

CPMD and Metadynamic learning

CPMD
Q1: Can CPMD generate Free energy surface? With MetaD or Umbrella sampling?
Q2: What is meaning of collective variables? fictitious mass? fictitious energy?
        Is it a function of coordinate R (nuclear position)?
Q3: what is the meaning of 1/2(s_i(R)-s_i)^2? Is the deviation of original s_i?
Q4: V(t,s) potential = integration along trajectories.

Ionic liquid learning

Compound: imidazole

Propargyl


dicyanamide: in IL, it should be an anion.

A one real IL propellant: 1-propargyl-3-methyl-imidazolium dicyanamide with WFNA (white fuming nitric acid)

How to use WHAM to obtain a free energy curve

WHAM is a program to be used to generate an relative free energy (FE) curve. Relative means you need specify a reference as zero.
1. Install WHAM.
2. Run your umbrella sampling (US) molecular dynamics simulations with PLUMED add-in. You should have a series of results. For example, if you want to obtain FE vs distances, you need manually specify a series of distances and run US around these distances.
3. Once you have all the results, you can use following script (a bash file):
#!/bin/bash

usfile=wham_usfile
fesout=fes.out

rm -rf $usfile $fesout
points=500  #there are 500 points/COLVAR.

for file in shortp? longp? longp??; do

tail -n $points $file/COLVAR | awk '{print $1,$2}' > $file/whamcv;
##get k constant
kappa=`grep UMBRELLA $file/plumed.dat  | head -n 1 | awk '{print $5}'`
## get umbrella center
PV=`grep UMBRELLA $file/plumed.dat  | head -n 1 | awk '{print $7}'`
echo $file/whamcv $PV $kappa >> wham_usfile
done;

first=`sort -n -k2 wham_usfile | awk '{print $2}' | head -n 1 `
last=`sort -n -k2 wham_usfile | awk '{print $2}' | tail -n 1 `
num=`wc -l wham_usfile | awk '{print $1}'`

wham $first $last $num 0.0001 500 0 $usfile $fesout

## above line shows command, min, max, number of points, tolerance, points of sampling around one distance, US input file, free energy outputfile. 

4. The output file will look like below.
#Coor           Free    +/-             Prob            +/-
9.410909        0.000000        nan     0.112293        nan
9.592727        0.228147        nan     0.076523        nan
9.774545        0.130469        nan     0.090179        nan
9.956364        0.022609        nan     0.108106        nan
10.138182       0.309783        nan     0.066711        nan
10.320000       0.200620        nan     0.080147        nan
10.501818       0.169518        nan     0.084449        nan
10.683636       0.125105        nan     0.090995        nan
10.865455       0.268023        nan     0.071562        nan
11.047273       0.013260        nan     0.109818        nan
11.229091       0.016527        nan     0.109217        nan
#Window         Free    +/-  
#0      0.000000        nan
#1      0.140395        nan
#2      -0.095729       nan
#3      -0.155083       nan
#4      -0.186455       nan
#5      -0.196517       nan
#6      -0.188120       nan
#7      -0.159148       nan
#8      -0.103205       nan
#9      -0.011637       nan
#10     0.124413        nan

We can have a FE curve using the first part. At the same time, we can obtain the probability distribution function based on the Boltzmann distribution equation (the fourth column).

The last part: these are the final F values from the wham calculation, and can be used

for computing weighted averages for properties other than the free energy.

The default unit is kcal/mol.