Gromacs-Gaussin 联用计算QM-MM的问题

hhhnano

看到一个教程
按照教程装了Gromacs-2018和GAUSSIAN09，在G09目录下放了Gromacs调用GAUSSIAN脚本gau, http://wwwuser.gwdg.de/~ggroenh/gau
设置好后，按照教程步骤进行QM-MM计算，Gromacs能正常计算结束，但是gaussin输出log文件有错误信息，Error termination via Lnk1e in /home/xzhfood/gaussian/g09/l101.exe, 网上搜索原因是gaussian输入文件中坐标后少了一个空行，查看了输入中间文件 input.com,发现有空行，但是内存为%mem=50000000，不知道从哪个文件调用的，我的输入文件设置内存为1GB，不知什么原因，特请教大家，非常感谢！
input.com文件信息：

%chk=input
%mem=50000000
%subst l701 /l701
%subst l301 /l301
%subst l9999 /l9999
#T  B3LYP/6-31G* Charge  guess=read
Nosymm units=bohr
FORCE Punch=(Derivatives) iop(3/33=1)

input-file generated by gromacs

0 1
  7 36.7381638  29.8613095  28.2966112
  1 32.5753840  27.0955281  32.2130708
  6 41.2017617  34.2618558  27.3917665
  1 46.3833225  31.4880863  34.1851549
  6 41.4451871  34.1362572  27.2594299
  1 42.2873023  36.2537346  34.3093208
  1 40.6567950  32.3938365  25.2137559
  8 42.9444189  36.7305923  28.6139599
  1 43.3785288  37.8532647  32.1377463
  6 44.5414596  29.9963944  28.9314753
  8 42.6837826  30.2887941  32.3197105
  7 42.6214721  32.1793046  31.4005092
  1 53.1943407  35.4598324  23.1180195
  6 47.6986549  33.6568651  27.3045363
  1 48.6866253  26.9531421  23.8650763
  1 55.2320694  24.6352303  39.2620809
  6 46.8012803  36.7122934  31.1972094
  8 43.0739328  37.8337560  31.2444942
  1 36.5448075  28.5439405  26.9310338
  1 48.7819563  36.3328280  31.4100945

21.5002829  20.5770222  23.1686924   0.1414
21.7814573  19.6415900  21.5593090   0.1997
22.5766820  19.7207599  24.5052659   0.1997
19.6392809  20.4928242  23.6509544   0.1997




屏幕输出信息：
。。。。。。
nr mm atoms in gaussian.c = 57
Calling '/home/xzhfood/gaussian/g09/gau < input.com > input.log'
Error: segmentation violation
   rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
   rdx 000000000000628b, rsp 00007ffcdb0ffc38, rbp 00007ffcdb1001b0
   rsi 000000000000000b, rdi 000000000000628b, r8  00002abfdbdad2c0
   r9  0000000000000000, r10 00007ffcdb0ff660, r11 0000000000000202
   r12 0000000000000000, r13 0000000000000000, r14 00007ffcdb1001f8
   r15 00000000000003e6
  /lib64/libpthread.so.0(+0xf5f0) [0x2abfdbf9a5f0]
  /lib64/libc.so.6(kill+0x7) [0x2abfdc4df607]
  /home/xzhfood/gaussian/g09/l101.exe() [0x45bfe7]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4672e9]
  /home/xzhfood/gaussian/g09/l101.exe() [0x48013d]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4701d0]
  /home/xzhfood/gaussian/g09/l101.exe() [0x46fcac]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4a66c2]
  /home/xzhfood/gaussian/g09/l101.exe() [0x40a54f]
  /home/xzhfood/gaussian/g09/l101.exe() [0x405f0f]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4037b0]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4036ed]
  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2abfdc4cb505]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4035e9]
nr mm atoms in gaussian.c = 57
Calling '/home/xzhfood/gaussian/g09/gau < input.com > input.log'
Error: segmentation violation
   rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
   rdx 00000000000062ab, rsp 00007ffdd663f648, rbp 00007ffdd663fbc0
   rsi 000000000000000b, rdi 00000000000062ab, r8  00002b57e692a2c0
   r9  0000000000000000, r10 00007ffdd663f060, r11 0000000000000206
   r12 0000000000000000, r13 0000000000000000, r14 00007ffdd663fc08
   r15 00000000000003e6
  /lib64/libpthread.so.0(+0xf5f0) [0x2b57e6b175f0]
  /lib64/libc.so.6(kill+0x7) [0x2b57e705c607]
  /home/xzhfood/gaussian/g09/l101.exe() [0x45bfe7]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4672e9]
  /home/xzhfood/gaussian/g09/l101.exe() [0x48013d]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4701d0]
  /home/xzhfood/gaussian/g09/l101.exe() [0x46fcac]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4a66c2]
  /home/xzhfood/gaussian/g09/l101.exe() [0x40a54f]
  /home/xzhfood/gaussian/g09/l101.exe() [0x405f0f]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4037b0]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4036ed]
  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b57e7048505]
  /home/xzhfood/gaussian/g09/l101.exe() [0x4035e9]

Writing final coordinates.

Back Off! I just backed up nvt.gro to ./#nvt.gro.13#

               Core t (s)   Wall t (s)        (%)
       Time:      110.801      110.801      100.0
                 (ns/day)    (hour/ns)
Performance:        0.158      152.367

GROMACS reminds you: "If at first you don't succeed, try two more times so that your failure is statistically significant." (Dallas Warren)

sobereva

目前的GROMACS都已经彻底把QMMM接口砍了，与其折腾这个还不如用Amber或NAMD，原生就支持QM/MM而且做得不错

hhhnano

谢谢SOB老师，GROMACS貌似没有去掉QM/MM，我装GROMACS2020带QM/MM也没有问题，如果能将接口程序gau稍加修改就好了，gromacs速度很快啊！

diaok

hhhnano 发表于 2020-3-3 15:08
谢谢SOB老师，GROMACS貌似没有去掉QM/MM，我装GROMACS2020带QM/MM也没有问题，如果能将接口程序gau稍加修改 ...

速控步骤不在md那边吧，虽然我也喜欢用gmx

liuyuje714

gmx的qmmm快个锤子。