|
[求助]
Gromacs 氢键分析出现错误(gmx hbond -ac)
本人gromacs菜鸟,在使用gromacs的gmx hbond 分析氢键时,命令中的-ac每次都会出现段错误,求助各位大佬,请问这是为什么?应该怎么解决?感谢各位大佬!
使用的gromacs为5.1.5版单精度,已尝试过不同体系,不同力场,双精度版本等,但都出现段错误。
一下为终端输出信息:
Command line:
gmx hbond -f ../md.xtc -s ../md.tpr -num -ac -life -g -hbn
Reading file ../md.tpr, VERSION 5.1.5 (single precision)
Specify 2 groups to analyze:
Group 0 ( System) has 3951 elements
Group 1 ( Other) has 66 elements
Select a group: 1
Selected 1: 'Other'
Select a group: 1
Selected 1: 'Other'
Calculating hydrogen bonds in Other (66 atoms)
Found 11 donors and 16 acceptors
Making hbmap structure...done.
Reading frame 0 time 0.000
Will do grid-seach on 9x9x6 grid, rcut=0.35
Frame loop parallelized with OpenMP using 4 threads.
Last frame 30000 time 300000.000
Found 12 different hydrogen bonds in trajectory
Found 32 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
11/11
- Reduced number of hbonds from 12 to 12
- Reduced number of distances from 32 to 32
Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.1#
Average number of hbonds per timeframe 0.853 out of 88 possible
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
-------- -------- --- Thank You --- -------- --------
Doing autocorrelation according to the theory of Luzar and Chandler.
段错误 |
|