1 描述
genconf multiplies a given coordinate file by simply stacking them on top of each other, like a small child playing with wooden blocks. The program makes a grid of user defined proportions (-nbox), and interspaces the grid point with an extra space -dist.
When option -rot is used the program does not check for overlap between molecules on grid points. It is recommended to make the box in the input file at least as big as the coordinates + Van der Waals radius.
If the optional trajectory file is given, conformations are not generated, but read from this file and translated appropriately to build the grid.
2 文件
| option |
filename |
type |
description
|
| -f |
conf.gro |
Input |
Structure file: gro g96 pdb tpr tpb tpa
|
| -o |
out.gro |
Output |
Structure file: gro g96 pdb
|
| -trj |
traj.xtc |
Input, Opt. |
Trajectory: xtc trr trj gro g96 pdb cpt
|
3 其它选项
| option |
type |
default |
description
|
| -[no]h |
bool |
no |
Print help info and quit
|
| -nice |
int |
0 |
Set the nicelevel
|
| -nbox |
vector |
1 1 1 |
Number of boxes. 将分子像堆积木一样堆积起来，一般按从小到大的顺序定义 x y z 方向上的分子数，否则会出现分子间距离较近的情况。最后分子的个数为 x*y*z。
|
| -dist |
vector |
0 0 0 |
Distance between boxes
|
| -seed |
int |
0 |
Random generator seed, if 0 generated from the time
|
| -[no]rot |
bool |
no |
Randomly rotate conformations
|
| -[no]shuffle |
bool |
no |
Random shuffling of molecules
|
| -[no]sort |
bool |
no |
Sort molecules on X coord
|
| -block |
int |
1 |
Divide the box in blocks on this number of cpus
|
| -nmolat |
int |
3 |
Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system!
|
| -maxrot |
vector |
90 90 90 |
Maximum random rotation
|
| -[no]renumber |
bool |
yes |
Renumber residues
|
4 已知问题
- The program should allow for random displacement off lattice points.
5 参考文献
