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标题: 请教namd常规md问题 [打印本页]

作者
Author: zjx-leslie 时间: 2016-12-21 14:20
标题: 请教namd常规md问题
我做的体系是 DNA-protein复合体系，在用namd作常规动力学模拟时遇到下面问题，基本上是做几步就退出来了。我是第一次做带有DNA的体系，在生成DNA的psf时，所用的top文件力场参数，是用生成小配体参数的网站生成的， https://cgenff.paramchem.org/use ... hp#20161220/DT1.str。我这种方法不知是否正确，希望老师和大神们指教！
1 生成的log文件如下：TCL: Minimizing for 5000 steps
PRESSURE: 0 nan nan nan nan nan nan nan nan nan
GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
ETITLE:    TS          BOND       ANGLE       DIHED       IMPRP             ELECT          VDW    BOUNDARY          MISC       KINETIC             TOTAL          TEMP    POTENTIAL       TOTAL3       TEMPAVG          PRESSURE    GPRESSURE       VOLUME    PRESSAVG    GPRESSAVG

ENERGY:    0    38492.5804    10260.2250    6753.4884       53.7573       -303373.7267 9999999999.9999       0.0000       0.0000       0.0000    9999999999.9999       0.0000 9999999999.9999 9999999999.9999       0.0000    -9999999999.9999 -9999999999.9999 1147125.0000 -9999999999.9999 -9999999999.9999

OPENING EXTENDED SYSTEM TRAJECTORY FILE
MINIMIZER SLOWLY MOVING 84 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 1 nan nan nan nan nan nan nan nan nan
GPRESSURE: 1 nan nan nan nan nan nan nan nan nan
ENERGY:    1    38035.4674    10341.2508    6755.6451       52.8761       -303511.5435 9999999999.9999       0.0000       0.0000       0.0000    9999999999.9999       0.0000 9999999999.9999 9999999999.9999       0.0000    -9999999999.9999 -9999999999.9999 1147125.0000 -9999999999.9999 -9999999999.9999

MINIMIZER SLOWLY MOVING 88 ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 2 nan nan nan nan nan nan nan nan nan
GPRESSURE: 2 nan nan nan nan nan nan nan nan nan
ENERGY:    2    37646.6593    10492.2029    6761.0360       51.9328       -303218.2758 9999999999.9999       0.0000       0.0000       0.0000    9999999999.9999       0.0000 9999999999.9999 9999999999.9999       0.0000    -9999999999.9999 -9999999999.9999 1147125.0000 -9999999999.9999 -9999999999.9999

文件中最小化部分有问题，压力值出现了 nan，是怎么回事，nan是非数么？

2 output文件报错如下：

Exited with exit code 137.

Resource usage summary:

CPU time : 2540.00 sec.
Max Memory :    12202 MB
Max Swap :    13322 MB

Max Processes  :       19
Max Threads :       21

The output (if any) follows:

Fatal error in PMPI_Isend: Internal MPI error!, error stack:
PMPI_Isend(146): MPI_Isend(buf=0x258872068, count=168, MPI_BYTE, dest=1, tag=1375, MPI_COMM_WORLD, request=0x25887213c) failed
(unknown)(): Internal MPI error!

希望老师们指教

作者
Author: fhh2626 时间: 2016-12-21 15:20
DNA、蛋白质都有各自的参数，小分子就用那个网站的参数就行
nan是not a number，如果你的PBC设置正确的话，跑几步应该就会有数了

你这个错误像是MPI的错误，一般来说namd跑普通平衡不用mpi版的。在单机上就用单机版，在集群上就用infiniband的版本

作者
Author: zjx-leslie 时间: 2016-12-22 09:35

fhh2626 发表于 2016-12-21 15:20
DNA、蛋白质都有各自的参数，小分子就用那个网站的参数就行
nan是not a number，如果你的PBC设置正确的话 ...

多谢老师，问题已解决，我应该是DNA的参数生成的有问题。

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