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来围观啊新虫 (小有名气)
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[求助]
Gromacs 氢键分析出现错误（gmx hbond -ac）
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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 |
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2楼2020-01-14 02:43:12