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标题: 求助最小化时报错文件不全 [打印本页]

作者
Author: watermelon_ 时间: 2024-10-22 11:11
标题: 求助最小化时报错文件不全
模拟时，参考了amber的官网教程进行模拟https://ambermd.org/tutorials/basic/tutorial13/index.php
第五步最小化是输入了指令pmemd.cuda -O -i mini2.in -o mini2.out -p c_box.prmtop -c eq2.rst7 -r mini2.rst7 -inf mini2.info -ref eq2.rst7 -x mini2.dcd
发生报错

At line 783 of file /data/home/amber22_src/AmberTools/src/sander/mdread1.F90 (unit = 5, file = 'mini2.in')
Fortran runtime error: End of file

Error termination. Backtrace:
#0  0x1509d4264d11 in ???
#1  0x1509d4265859 in ???
#2  0x1509d426653f in ???
#3  0x1509d44a9c4b in ???
#4  0x1509d44aaf2c in ???
#5  0x1509d44ada8e in ???
#6  0x1509d44adcfc in ???
#7  0x1509d44ade57 in ???
#8  0x5639bdf2b4f6 in ???
#9  0x5639bdef7fd0 in ???
#10  0x5639bdef705c in ???
#11  0x5639bdef70b8 in ???
#12  0x1509d4059082 in __libc_start_main
      at ../csu/libc-start.c:308
#13  0x5639bdd2aded in ???
#14  0xffffffffffffffff in ???

这里使用的mini2.in文件是
Minimization of everything excluding backbone
&cntrl
  imin = 1, maxcyc = 1000,
  ncyc = 30, ntx = 1,
  ntwe = 0, ntwr = 500, ntpr = 50,
  ntc = 2, ntf = 2, ntb = 1, ntp = 0,
  cut = 10.0,
  ntr=1, restraintmask = "@CA,N,C,P",
  restraint_wt = 10.,
  ioutfm=1, ntxo=2,
/
感觉这个文件没有缺漏呀
然后用mpirun -np 32 sander -O -i mini2.in -o mini2.out -p c_box.prmtop -c eq2.rst7 -r mini2.rst7 -inf mini2.info -ref eq2.rst7 -x mini2.dcd试了试，还是这个报错
请问怎么解决呐

作者
Author: watermelon_ 时间: 2024-10-22 11:21
运行sander -O -i mini2.in -o mini2.out -p c_box.prmtop -c eq2.rst7 -r mini2.rst7 -inf mini2.info -ref eq2.rst7 -x mini2.dcd
log里面记录的是
4.  RESULTS
--------------------------------------------------------------------------------

---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
nfft1-3 too large! check on MAXNFFT in ew_bspline.f

在in文件末尾加了几行
&ewald
  nfft1 = 128, ! 根据需要选择合适的值
  nfft2 = 128,
  nfft3 = 128,
/

然后运行sander -O -i mini2.in -o mini2.out -p c_box.prmtop -c eq2.rst7 -r mini2.rst7 -inf mini2.info -ref eq2.rst7 -x mini2.dcd

还是最先那个报错怎么办~~~
At line 1978 of file /data/home/amber22_src/AmberTools/src/sander/ew_setup.F90 (unit = 5, file = 'mini2.in')
Fortran runtime error: End of file

Error termination. Backtrace:
#0  0x154555beed11 in ???
#1  0x154555bef859 in ???
#2  0x154555bf053f in ???
#3  0x154555e33c4b in ???
#4  0x154555e34f2c in ???
#5  0x154555e37a8e in ???
#6  0x154555e37cfc in ???
#7  0x154555e37e57 in ???
#8  0x555ce2b7be9d in ???
#9  0x555ce2b80f7b in ???
#10  0x555ce2b28fca in ???
#11  0x555ce2af3fd0 in ???
#12  0x555ce2af305c in ???
#13  0x555ce2af30b8 in ???
#14  0x1545559e3082 in __libc_start_main
      at ../csu/libc-start.c:308
#15  0x555ce2926ded in ???
#16  0xffffffffffffffff in ???

作者
Author: watermelon_ 时间: 2024-10-22 11:40
in文件末尾加了一个换行
现在可以跑了
：）

作者
Author: watermelon_ 时间: 2024-10-22 11:41
已解决

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