三种常用分子模拟软件介绍

export PATH=$$PATH:/home/gromacs-3.3.1/bin ( append

to .bashrc)

(6)

编译

gromacs

源包里的其它文件（可选）

make contrib

注：这步可以省去

update: gromacs -4.0

，

fftw-3.2.1

，< /p>

lam7.1.4

与上面的方法完全相

同 ，只需更换目录即可。

模拟步骤

Below is presented a generalised procedure for performing a

simulation. The exact steps and processes involved will vary

depending on exactly what is being attempted. Use as a general

guide only!

1> Clearly identify the property / phenomena of interest to be

studied by performing the simulation.

2>Select the appropriate tools to be able to perform the

simulation and observe the property/phenomena of interest. It is

important to read and familiarise yourself with publications by other

researchers on similar systems. Tools include: - software to perform

the simulation with, consideration of force field may influence this

decision.- force field which describes how the atoms / particles within

the system interact with each other. Select one that is appropriate for

the system being studied and the property/phenomena of interest.

Very important and non- trivial step!

3>Obtain/generate the initial coordinate file for each molecule to

be placed within the system.

4>Generate the raw starting structure for the system by placing

the molecules within the coordinate file as appropriate. Molecules

may be specifically placed or arranged randomly.

5>Obtain/generate the topology file for the system, using (for

example) pdb2gmx, PRODRG or your favourite text editor in concert

with chapter 5 of the GROMACS Manual.

6>Describe a simulation box (e.g. using editconf) whose size is

appropriate for the eventual density you would like, fill it with solvent

(e.g. using genbox), and add any counter-ions needed to neutralize

the system (e.g. using grompp and genion). In these steps you may

need to edit your topology file to stay current with your coordinate file.

7>Run an energy minimisation simulation on the system (using

grompp and mdrun). This is required to sort out any bad starting

structures caused during generation of the system, which may cause

the production simulation to crash.

8>Select the appropriate simulation parameters for the

equilibration simulation (defined in .mdp file). You need to be

consistent with how force field was derived. You may need to simulate

at NVT with position restraints on your solvent and/or solute to get the

T almost right, then relax to NPT to fix the density, then move further

(if needed) to reach your production simulation ensemble (e.g. NVT,

NVE).

9>Run the equilibration simulation for sufficient time so that the

system relaxes sufficiently to allow the production run to be

commenced (using grompp and mdrun, then g_energy and trajectory

visualisation tools).

10>Select the appropriate simulation parameters for the

production simulation (defined in .mdp file), in particular be careful not

to re-generate the velocities. You still need to be consistent with how

the force field was derived and how to measure the property /

phenomena of interest.

11>Run the production simulation for sufficient time so that

property / pheno-mena of interest can be observed in required detail

(using grompp/tpbconv and mdrun).

12>Analyse / visualise the resulting trajectory and data files to

obtain information on the property / phenomena of interest. [4]

三、

Amber

Amber

是著名的分子动力学软件，

用于蛋白质、

核酸、

糖等生物大分子

的计算模拟。