一、 Ethane-to-ethane “zero-sum” transformation

步骤：编写pgn文件--创建alch.file（fep文件）--运行namd2模拟计算（生成fepout文件）--运行parsefep（生成parsefeplog文件）

1、编写pgn文件（用于做psf文件）

cd C:/Users/lxf/Desktop/FEP-tutorial-files/ethane-ethane
ps：文件名称不能有“."
写了pgn文件
导入：>Main< (ethane-ethane) 9 % source setup.pgn
MOLECULE MISSING! Use resetpsf to start over.
topology时候，后面跟了路径就报上错，方法是直接把立场文件拖到文件夹下面，就可以了。
返回信息，并且生成两个文件：
psfgen) Info: writing psf file setup.psf
psfgen) total of 1030 atoms
psfgen) total of 690 bonds
psfgen) total of 366 angles
psfgen) total of 30 dihedrals
psfgen) total of 0 impropers
psfgen) total of 0 cross-terms
psfgen) Info: psf file complete.
psfgen) Info: writing pdb file setup.pdb
psfgen) Info: pdb file complete.

2、创建alch.file

you will create the alchFile. Recall that the system you have created contains a) atoms in the initial state that will gradually vanish, b) atoms that will gradually appear towards the final state, and c) atoms that are present throughout the whole transformation. NAMD distinguishes between these three classes of atoms based on information in the alchFile. The alchFile is essentially the PDB file of your system, except that every atom has been tagged according to the class to which it belongs.
（1)pdb文件修改fixcdatom那一列，变动位置的均改为1；
（2）另存为.zero.fep文件；
（3)运行：vmd setup.psf -pdb zero.fep

image.png
修改显示

ps：NAMD2.7b2或更高版本可以使用这个命令alchemify setup.psf zero.psf zero.fep但是这个命令会闪退。不知道。
缺一个截图

3、Running the free energy calculation

三行命令，cd，namd2,namd2,后生成forward相关文件和backword相关文件若干。
C:\Users\lxf>cd C:/Users/lxf/Desktop/FEP-tutorial-files/NAMD
C:\Users\lxf\Desktop\FEP-tutorial-files\NAMD>namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/ethane-ethane/forward-noshift.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/ethane-ethane/forward-noshift.log
C:\Users\lxf\Desktop\FEP-tutorial-files\NAMD>namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/ethane-ethane/backward-noshift.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/ethane-ethane/backward-noshift.log
FATAL ERROR: Exiting prematurely; see error messages above.
报错中断重启再运行一次就可以了。

namd2运行成功生成文件
image.png

4、results

image.png

BAR-estimator: total free energy change is 0.5219198381032337 , total error is 0.42174463270676
生成parseFEP.log文件（生成在VMD文件夹中）

问题： parsefep文件生成的plot

5、a soft-core potential

The parameters utilized for the soft-core potential are rather detailed and can be somewhat confusing, so be sure to read the following carefully. Outgoing atoms will see their electrostatic interactions with the environment decoupled during = 0 to 1 − alchElecLambdaStart = 0.5, while the interactions involving incoming atoms are progressively coupled during = 1 −alchElecLambdaStart to 1.λλ
At the same time, van der Waals interactions involving vanishing atoms are progressively decoupled during = 1 − alchVdwLambdaEnd, i.e. 0 to 1, while the interactions of appearing atoms with the environment become coupled during = 1 to 1 −alchVdwLambdaEnd, i.e. 0.λλ

forward-shift.namd和noshift的区别

第三步是namd2 noshift文件
第五步是namd2 shift文件

soft_core
运行3行命令：cd,namd2 forward-shift,namd2 back-shift
cd C:/Users/lxf/Desktop/FEP-tutorial-files/NAMD
namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/ethane-ethane/forward-shift-long.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/ethane-ethane/forward-shift.log

namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/ethane-ethane/backward-shift.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/ethane-ethane/backward-shift.log
运行报错
forward-shift-long运行页报错，运行中断，重启也不行。
未生成fepout文件，无法在vmd中parsefep生成parsefep.log文件，从而无法做出plot图。

这个图是16个数据做出来的，有待解决

二、Charging a spherical ion

Our system consists of a sodium ion immersed in a bath of water molecules. Using the dual-topology paradigm, we could charge a Lennard-Jones particle by shrinking a naked spherical particle, while growing concomitantly the ion.

1、编写setup.pgn文件（source...，生成setup.psf和pdb文件）

Generate the PSF and PDB files for the system, which is a sodium ion SOD at the center of a water box.
source setup.pgn

2、调用solvate软件包

把setup.psf和pdb所储存的放在一个water.box。

Main< (charging-spherical-ion) 4 % package require solvate
1.6
Main< (charging-spherical-ion) 5 % solvate setup.psf setup.pdb -t 15 -o solvate

image.png

3、创建solvate.fep文件（修改pdb的fixedatom列）

OD SOD S 1 0.000 0.000 0.000 1.00 1.00 SOD NA

4、Running the free energy calculation

cd到工作目录
C:\Users\lxf>cd C:/Users/lxf/Desktop/FEP-tutorial-files/NAMD
namd2平衡系统
C:\Users\lxf\Desktop\FEP-tutorial-files\NAMD>namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/charging-spherical-ion/equilibration.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/charging-spherical-ion/equilibration.log
namd2 forward
C:\Users\lxf\Desktop\FEP-tutorial-files\NAMD>namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/charging-spherical-ion/forward.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/charging-spherical-ion/forward.log
namd2 backward
C:\Users\lxf\Desktop\FEP-tutorial-files\NAMD>namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/charging-spherical-ion/backward.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/charging-spherical-ion/backward.log
生成若干文件，主要有forward和backward的fepout文件。
parsefep，得到如下结论：
BAR-estimator: total free energy change is -78.50647874138971 , total error is 0.36116460557554414
生成parsefep.log文件在工作目录下。

三、Mutation of tyrosine into alanine酪氨酸突变为丙氨酸

In this section, we will calculate the free energy change involved in the point mutation of the N- and Cterminally blocked Ala–Tyr–Ala tripeptide. Our calculation will be based on the thermodynamic cycle of Figure 8. [19] We will calculate the quantities. and. by running two FEP simulations
of the mutation, one in vacuo and the other in bulk water. This case is a computationally affordable
example of how point mutations in more complex protein systems may be studied.In this section, we will calculate the free energy change involved in the point mutation of the N- and Cterminally blocked Ala–Tyr–Ala tripeptide. Our calculation will be based on the thermodynamic cycle of Figure 8. [19] We will calculate the quantities. and. by running two FEP simulations
of the mutation, one in vacuo and the other in bulk water. This case is a computationally affordable
example of how point mutations in more complex protein systems may be studied.

酪氨酸Tyr， image.png
丙氨酸Ala， image.png

1、编写pgn文件（对照例1）

cd C:/Users/lxf/Desktop/FEP-tutorial-files/Mutating-tyrosine-into-alanine
pgn中，segment{first ACE last CT3 }删除了，不然就报错building segment失败。
source setup.pgn
生成了y2a.pdb/psf.

2、Create the alchFile

y2a.pdb的Bcol，17--35，改为1.另存为y2a.fep
vmd y2a.psf -pdb y2a.fep
In the Graphics/Representations menu, set the coloring method to Beta。

问题：无绿色

出现的丙氨酸侧链应为蓝色，酪氨酸侧链应为红色，而主链和两个未受干扰的丙氨酸残基应为绿色。
alchemify y2a.psf y2a-alch.psf y2a.fep该命令又闪退了。

3、放入水系统中

（1) vmd y2a.psf y2a.pdb

image.png

(2)Open the Solvate interface (Extensions/Modeling/Add Solvation Box).

image.png
image.png

(3)创建新的alch.file，修改solvate.pdb的B，17--35，0改为1，另存为solvate.fep
vmd solvate.psf -pdb solvate.fep这个命令也卡
al...那个命令依旧闪退。

4、模拟

（1）in vacuo真空
3个命令，cd，namd2平衡，namd2 forward,namd2 backward.
生成forward.fepout和backward.fepout文件
parsefep制作以上两个文件，生成parsefep.log文件。
Main< (lxf) 10 % cd C:/Users/lxf/Desktop/FEP-tutorial-files/Mutating-tyrosine-into-alanine/In-vacuo

Main< (In-vacuo) 11 % namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/Mutating-tyrosine-into-alanine/In-vacuo/equilibrate.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/Mutating-tyrosine-into-alanine/In-vacuo/equilibrate.log
FATAL ERROR: UNABLE TO OPEN .psf FILE y2a.psf
Main< (In-vacuo) 12 % namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/Mutating-tyrosine-into-alanine/In-vacuo/equilibrate.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/Mtating-tyrosine-into-alanine/In-vacuo/equilibrate.log
FATAL ERROR: UNABLE TO OPEN .psf FILE y2a.psf
(2)in aqua
cd C:/Users/lxf/Desktop/FEP-tutorial-files/NAMD
Main< (NAMD) 15 % namd2 C:/Users/lxf/Desktop/FEP-tutorial-files/Mutating-tyrosine-into-alanine/In-aqua/equilibrate.namd > C:/Users/lxf/Desktop/FEP-tutorial-files/Mutating-tyrosine-into-alanine/In-aqua/equilibrate.log
child killed: segmentation violation不知道是不是报错
namd2 forward-off,失败，FATAL ERROR: Unable to open extended system file.
namd2 backward-off