[经验心得] Gromacs使用－新手入门篇 相关搜索: gromacs, 入门

iamjoan0928

其实gromacs的思路比较简单，大体就是以下的流程,在此先对em进行一下总结：


1.  convert the pdb-file to a gromacs structure file(.gro / .pdb) and a gromacs topology file(.top)
这一步需要gromacs的预处理程序pdb2gmx
标准的输入命令应该是：
＃ pdb2gmx -ignh -f speptide.pdb -p speptide.top -o speptide.gro
这个命令之后有一个force field 的选择 系统给出了11种力场，具体以后实际计算中如何选择力场还是应该多参阅文献和gromacs说明书的。
这步之后可以在屏幕看到：

--------- PLEASE NOTE ------------
You have succesfully generated a topology from: speptide.pdb.
The G43a1 force field and the spc water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0

--------- ETON ESAELP ------------至此，完成了从pdb到gro和top的转变。另外，我也看过有的作这一步命令时候并不进行top文件的转换，因为在genbox（对盒子加水溶剂化时还要对top文件进行修改）
2.  solvate the peptide in water
这一步需要用到editconf和genbox两个程序，命令的标准书写应该是：
# editconf -bt cubic -f speptide.gro -o speptide_box.gro -c -d 0.5
可以在屏幕上看到
Read 191 atoms
Volume: 8.17315 nm^3, corresponds to roughly 3600 electrons
No velocities found

system size :
1.774
3.372
1.367 (nm)

diameter
:
3.517
(nm)

center
:
2.650
1.453
2.417 (nm)

box vectors :
1.774
3.372
1.366 (nm)

box angles
:
90.00
90.00
90.00 (degrees)

box volume
:
8.17
(nm^3)

shift
: -0.391
0.806 -0.158 (nm)
new center
:
2.259
2.259
2.259 (nm)
new box vectors :
4.517
4.517
4.517 (nm)
new box angles
:
90.00
90.00
90.00 (degrees)
new box volume
:
92.18
(nm^3)


因为程序的默认，所以这一步命令可以写作：
# editconf –f speptide –o –d 0.5
这里－f之后的sp文件是默认gro文件或者pdb文件，－o后面生成的output file是放入盒子的体系的gro文件 按照这样的格式，输出的文件被默认命名为－out.gro


体系放入盒子之后在盒子中注入水
# genbox -cp speptide_box.gro -cs -p speptide.top -o speptide_water.gro
也可简写为 ：
# genbox –cp out –cs –p sprptide –o b4em
Screen--
Output configuration contains 9035 atoms in 2967 residues
Volume
:
92.1813 (nm^3)
Density
:
994.449 (g/l)
Number of SOL molecules:
2948



之后看加水之后的top文件 用命令 #
tail speptide.top
可以看到

[ system ]
; Name
Protein in water


[ molecules ]
; Compound
#mols
Protein
1
SOL
2948
其中SOL后面的数字2948就是genbox加入盒子的水分子的数目。
Editconf程序的另一个用途是讲gro文件转化回pdb 这时可以讲speptide_water.gro转化回pdb观察
＃ editconf –f speptide_water.gro –o speptide.pdb
拖回本机 用spbdv或者vmd观察 。
The next step is to generate index file . in the tutor of
gromacs , we are told that there are a set of index groups to select, unfortunately, I didi not find them ,so I have to use make_ndx to generate one .
# make_ndx –f b4em


3.  perform an enery minimization of the peptide in solvent
Now the simulation system is almost ready. Before we can start the dynamics, we must perform an energy minimization, to alleviate any bad contacts (atoms overlapping such that a significant repulsion would result, causing numerical problems in the simulation) that might be present in the system.
# grompp –v –f em.mdp –c speptide_water.gro –p speptide.top –o speptide_em.tpr
Or use this command for short:
# grompp –v –f em –c b4em –p speptide –o em
After this command ,the bad contacs have been removed .so we can do enery minimization now.
# mdrun –v –s speptide_em.tpr –o speptide_em.trr –c after_em.gro –g emlog.log
Or
# mdrun –v –s em –o em –c after_em –g emlog
From screen ,we can see these ------

Steepest Descents:

Tolerance (Fmax)
=
2.00000e+03

Number of steps
=
100
Step=
0, Dmax= 1.0e-02 nm, Epot= -8.02562e+04 Fmax= 2.70468e+04, atom= 6792
Step=
1, Dmax= 1.0e-02 nm, Epot= -8.69641e+04 Fmax= 1.24531e+04, atom= 6657
Step=
2, Dmax= 1.2e-02 nm, Epot= -9.48067e+04 Fmax= 5.54072e+03, atom= 9009
Step=
3, Dmax= 1.4e-02 nm, Epot= -1.02743e+05 Fmax= 2.86957e+03, atom= 8766
Step=
4, Dmax= 1.7e-02 nm, Epot= -1.08941e+05 Fmax= 1.53075e+04, atom= 150
Step=
5, Dmax= 2.1e-02 nm, Epot= -1.10083e+05 Fmax= 1.31653e+04, atom= 150
Step=
6, Dmax= 2.5e-02 nm, Epot= -1.10564e+05 Fmax= 2.16454e+04, atom= 150
Step=
7, Dmax= 3.0e-02 nm, Epot= -1.11528e+05 Fmax= 1.82398e+04, atom= 150
Step=
9, Dmax= 1.8e-02 nm, Epot= -1.12767e+05 Fmax= 3.87548e+03, atom= 120
Step=
11, Dmax= 1.1e-02 nm, Epot= -1.13598e+05 Fmax= 1.23013e+04, atom= 120
Step=
12, Dmax= 1.3e-02 nm, Epot= -1.14464e+05 Fmax= 5.37656e+03, atom= 120
Step=
13, Dmax= 1.5e-02 nm, Epot= -1.14787e+05 Fmax= 1.74494e+04, atom= 120
Step=
14, Dmax= 1.9e-02 nm, Epot= -1.15874e+05 Fmax= 8.35820e+03, atom= 120
Step=
16, Dmax= 1.1e-02 nm, Epot= -1.16420e+05 Fmax= 6.65421e+03, atom= 120
Step=
17, Dmax= 1.3e-02 nm, Epot= -1.16807e+05 Fmax= 1.08106e+04, atom= 120
Step=
18, Dmax= 1.6e-02 nm, Epot= -1.17248e+05 Fmax= 1.12834e+04, atom= 120
Step=
19, Dmax= 1.9e-02 nm, Epot= -1.17425e+05 Fmax= 1.45145e+04, atom= 120
Step=
20, Dmax= 2.3e-02 nm, Epot= -1.17590e+05 Fmax= 1.67089e+04, atom= 120
Step=
22, Dmax= 1.4e-02 nm, Epot= -1.18845e+05 Fmax= 2.65542e+03, atom= 121
Step=
23, Dmax= 1.7e-02 nm, Epot= -1.19198e+05 Fmax= 2.39072e+04, atom= 120
Step=
24, Dmax= 2.0e-02 nm, Epot= -1.20588e+05 Fmax= 6.17310e+03, atom= 120
Step=
26, Dmax= 1.2e-02 nm, Epot= -1.20901e+05 Fmax= 1.04224e+04, atom= 120
Step=
27, Dmax= 1.4e-02 nm, Epot= -1.21229e+05 Fmax= 8.89909e+03, atom= 120
Step=
28, Dmax= 1.7e-02 nm, Epot= -1.21346e+05 Fmax= 1.51125e+04, atom= 120
Step=
29, Dmax= 2.1e-02 nm, Epot= -1.21686e+05 Fmax= 1.29390e+04, atom= 120
Step=
31, Dmax= 1.2e-02 nm, Epot= -1.22216e+05 Fmax= 3.21419e+03, atom= 120
Step=
33, Dmax= 7.5e-03 nm, Epot= -1.22523e+05 Fmax= 6.52631e+03, atom= 120
Step=
34, Dmax= 8.9e-03 nm, Epot= -1.22796e+05 Fmax= 6.31916e+03, atom= 120
Step=
35, Dmax= 1.1e-02 nm, Epot= -1.22998e+05 Fmax= 8.04922e+03, atom= 120
Step=
36, Dmax= 1.3e-02 nm, Epot= -1.23167e+05 Fmax= 9.93619e+03, atom= 120
Step=
37, Dmax= 1.5e-02 nm, Epot= -1.23317e+05 Fmax= 1.10029e+04, atom= 120
Step=
39, Dmax= 9.3e-03 nm, Epot= -1.23857e+05 Fmax= 1.88770e+03, atom= 810


writing lowest energy coordinates.


Steepest Descents converged to Fmax < 2000 in 40 steps
Potential Energy
= -1.2385705e+05
Maximum force
=
1.8876959e+03 on atom 81
Norm of force
=
1.3663420e+04
NOTICE!!!!!!!!!
If the potential enery after minimization is lower than -1.1e+05kJ/mol, it is acceptable and the structure can be used for MD caculations.


[ 本帖最后由 iamjoan0928 于 2008-7-1 09:24 编辑 ]

tecpenguin

这是能量最优化部分，下一部分我来补充吧。

anquren

原帖由 tecpenguin 于 2008-7-1 09:44 发表
这是能量最优化部分，下一部分我来补充吧。

期盼着

qugm110

:D:

smartgyg

能介绍一下Gromacs有什么作用？可以处理那些问题？

tecpenguin

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition:

    * GROMACS provides extremely high performance compared to all other programs. A lot of algorithmic optimizations have been introduced in the code; we have for instance extracted the calculation of the virial from the innermost loops over pairwise interactions, and we use our own software routines to calculate the inverse square root. The innermost loops are generated automatically in either C or Fortran at compile time, with optimizations adopted to your architecture. Assembly loops using SSE and 3DNow! multimedia instructions are provided for i386 processors, separate versions using all x86-64 registers are used on Opteron x86-64 and Xeon EM64t machines. This results in exceptional performance on inexpensive PC workstations, and for Pentium IV/Opteron processors there are also SSE2 double precision assembly loops. There are new manually tuned assembly loops for ia64 (both single and double precision), and last but certainly not least we have written Altivec assembly loops both for Linux and Mac OS X. Gromacs is normally 3-10 timesfaster than any other program; check the article in Journal of Molecular Modeling (reference can be found under resources) for a comparison benchmark.

    * GROMACS is user-friendly, with topologies and parameter files written in clear text format. There is a lot of consistency checking, and clear error messages are issued when something is wrong. Since the C preprocessor is used, you can have conditional parts in your topologies and include other files. You can even compress most files and GROMACS will automatically pipe them through gzip upon reading.

    * There is no scripting language - all programs use a simple interface with command line options for input and output files. You can always get help on the options by using the -h option, or use the extensive manuals provided free of charge in electronic or paper format. There is also an integrated graphical user interface available for all programs.

    * As the simulation is proceeding, GROMACS will continuously tell you how far it has come, and what time and date it expects to be finished.

    * Both run input files and trajectories are independent of hardware endian and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision. All files from GROMACS 2.0 can further be used in the new version 3!

    * GROMACS can write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user.

    * GROMACS comes with a large selection of flexible tools for trajectory analysis - you won't have to write any code to perform routine analyses. The output is further provided in the form of finished Xmgr/Grace graphs, with axis labels, legends, etc. already in place!

    * A basic trajectory viewer that only requires standard X libraries is included, and several external visualization tools can read the GROMACS file formats.

    * GROMACS can be run in parallel, using standard MPI communication.

    * GROMACS contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail.

    * The package includes a fully automated topology builder for proteins, even multimeric structures. Building blocks are available for the 20 standard aminoacid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide resides, several sugars and lipids, and some special groups like hemes and several small molecules.

    * There is ongoing development to extend GROMACS with interfaces both to Quantum Chemistry and Bioinformatics/databases.

    * GROMACS is Free Software, available under the GNU General Public License.

suny2005

能不能介绍一下用gromacs怎样计算非生物体系？包括如何修改力场，建结构文件，以及后面的运算？

tecpenguin

这个的内容很多，而且不同的力场修改的内容的方式不一样，有具体的问题可以发上来问

shabeir

谢谢

childs

学习中 期待后面的部分 希望有对轨迹的分析
问一句 命令缩写中的b4em是什么意思？非常感谢