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标题: gromacs模拟多糖mdrun途中段错误怎么办 [打印本页]

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Author: Sunca 时间: 2024-6-20 18:37
标题: gromacs模拟多糖mdrun途中段错误怎么办
多糖链结构文件是由charmm-gui网站生成的，top文件由pdb2gmx命令得到，力场是charmm36,其中糖残基rtp文件我是用charmm-gui网站的itp文件自己写的,经过steep+cg能量最小化、nvt退火，npt平衡到正式模拟，前面都没什么问题，但正式模拟到几千万步就会突然段错误停掉，根据sob老师在思想家公社的思路排查了，但我实在找不到原因在哪。各文件我都上传附件了，希望有大佬帮忙耐心看看问题出在哪。
starting mdrun 'Protein in water'
100000000 steps, 100000.0 ps.
step 37000: timed with pme grid 96 28 28, coulomb cutoff 1.200: 36.4 M-cycles
step 37200: timed with pme grid 84 25 25, coulomb cutoff 1.278: 38.4 M-cycles
step 37400: timed with pme grid 72 20 20, coulomb cutoff 1.536: 46.7 M-cycles
step 37600: timed with pme grid 72 24 24, coulomb cutoff 1.491: 44.8 M-cycles
step 37800: timed with pme grid 80 24 24, coulomb cutoff 1.342: 42.1 M-cycles
step 38000: timed with pme grid 84 24 24, coulomb cutoff 1.280: 38.7 M-cycles
step 38200: timed with pme grid 84 25 25, coulomb cutoff 1.278: 52.5 M-cycles
step 38400: timed with pme grid 96 25 25, coulomb cutoff 1.229: 37.3 M-cycles
step 38600: timed with pme grid 96 28 28, coulomb cutoff 1.200: 38.1 M-cycles
            optimal pme grid 96 28 28, coulomb cutoff 1.200
step 12212400, will finish Thu Jun 20 02:45:44 2024段错误

修改的糖残基rtp
[ BM2A ]
; 2-o-acetyl-beta-D-mannose
  [ atoms ]
   C1 CC3162  0.2900 1
   H1    HCA1  0.0900 1
   C5 CC3163  0.1100 1
   H5    HCA1  0.0900 1
   O5 OC3C61 -0.4000 1
   C2 CC3161  0.1700 2
   CY2 CC331 -0.3100 2
   HY21    HCA3  0.0900 2
   HY22    HCA3  0.0900 2
   HY23    HCA3  0.0900 2
   CX2 CC2O5  0.9000 2
   OX2 OC2D1 -0.6300 2
   H2    HCA1  0.0900 2
   O2 OC301 -0.4900 2
   C3 CC3161  0.1400 3
   H3    HCA1  0.0900 3
   O3 OC311 -0.6500 3
   HO3    HCP1  0.4200 3
   C4 CC3161  0.0900 4
   H4    HCA1  0.0900 4
   O4 OC301 -0.3600 4
   C6 CC321  0.0500 5
   H61    HCA2  0.0900 5
   H62    HCA2  0.0900 5
   O6 OC311 -0.6500 5
   HO6    HCP1  0.4200 5
  [ bonds ]
   C1 -O4
   C1 H1
   C1 O5
   C1 C2
   C2 H2
   C2 O2
   O2 CX2
   CX2 OX2
   CX2 CY2
   CY2  HY21
   CY2  HY22
   CY2  HY23
   C2 C3
   C3 H3
   C3 O3
   O3 HO3
   C3 C4
   C4 H4
   C4 O4
   O4 +C1
   C4 C5
   C5 H5
   C5 C6
   C6 H61
   C6 H62
   C6 O6
   O6 HO6
   C5 O5
  [ angles ]
C4 O4 +C1
  [ dihedrals ]
C5 C4 O4 +C1
C3 C4 O4 +C1
H4 C4 O4 +C1
C4 O4 +C1 +H1
C4 O4 +C1 +O5
C4 O4 +C1 +C2

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