Sensenbobo Blogging

化学键摩尔斯势能

在经验力场中，化学键势能表达方法是使用弹簧势能表达的。相对来说，摩尔斯化学键势能表示方法要准确一些。摩尔斯化学健势能表达为：

U(x) = D_e[1 - e^-(x-r_e)]²

其中，D_e为两个成健原子互相分离时的化学能量; x为两原子之间的相对距离; r_e为两原子的平衡位置。
摩尔斯势能图可以简单表示如下：

Adding Ions to MD systems

Before preforming you MD simulation, proteins should be solvated into a water box. Try not to run MD simulation in vacuum these days, update you computer or just apply for some computational resources to Nankai Stars. ^_^

If you use gromacs, you can use genion to add ions to you system. Actually, genion is quite stupid. It just place the ions around the protein, because it thinks that is the low potential energy solution. you can use the -random flag to place the added ions all around the system. if you find out some ions are too close to the protein, change the -seed flag until you think it is reasonable.

Amber suite have two commands to add ions into MD system: addions and addions2. Both of them have some drawbacks. addions just add ions around the protein, while addions2 add ions to the system at the edge of the bound box. I think addions2 is more reasonable, cause it does not cause some artificial effects. But if you add some positive ions and some negative ions at the same time using addions2, both positive and negative ions will be at the edge of the bound box, then after the energy minimization, they will bound to each other. that is too bad.

Too solve the addions/addions2 problems in amber suite, you can use addions to add some ions at first, and use addions2 at the second time to neutralize the system. Or you can solvate your protein a little bit, then use addions2 to add some ions, then fully solvate your system and use addions2 to neutralize the whole system.

And how about Namd? you can tell me. :D

How to Enlarge Your System Using Gromacs

When doing SMD, sometimes you do not want to do the energy minimizaton(em) and position restrain(pr) with a large system. So, you just solvate your protein into a water box a little bigger than your protein, like with 1.5 nanometer buffer distance.

So here is the question: what do you do after the free MD run before starting to pull? You can take you protein out of the water box and solvate if into a bigger water box of course, and do em and pr again. But still, you can do it in another way.

First of all, use the -translate flag of editconf to move your system, like 5 nm from it's original position, and elongate the side of the water box along which you want to pull your protein( You have your protein oriented right??). After that, use genbox to solvate all your system. ( Or you do not have to use the -translate flag, just use editconf to enlarge your water box.)

Second, use genion to add ions to your system. This is the most complicate party of the job. You can do it step by step like the following:

1. Change all the newly added water molecular in the .gro file to another group name, like WAT.

2.Edit the .top files. At the end of the .top file, you can see genbox have automaticly name your new added water molecular in a new SOL group just like the other water molecular. Change this SOL to WAT.

3. Make a topology file for residue WAT. Take tip4p for example, copy the tip4p.itp to some file name like tipppp.itp and change all SOL in it to WAT.

4.The last step, edit you system topology file to include tipppp.itp.

OK, You now can use grompp to make a tpr file and use genion to add ions to your system. Remember to choose the WAT group to ions.

And now, you can do much shorter time of em and pr , and just pull you protein. ^_^