在Ubuntu 16.04中运行NAMD

Question

我想在Ubuntu16.04中运行NAMD，但是遇到了以下错误。我怎么能解决这个问题？

nikoot@nikoot-GA-880GM-USB3:~$ namd2
Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID: v6.7.0-0-g46f867c-namd-charm-6.7.0-build-2015-Dec-21-45876
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.  
Charm++> scheduler running in netpoll mode.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD 2.11 for Linux-x86_64-TCP
Info: 
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info: 
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: 
Info: Based on Charm++/Converse 60700 for net-linux-x86_64-tcp-iccstatic
Info: Built Mon Dec 21 10:52:27 CST 2015 by jim on despina.ks.uiuc.edu
Info: 1 NAMD  2.11  Linux-x86_64-TCP  1    nikoot-GA-880GM-USB3  nikoot
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.01368 s
FATAL ERROR: No simulation config file specified on command line.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: No simulation config file specified on command line.

[0] Stack Traceback:
  [0:0] _Z8NAMD_diePKc+0x72  [0x640c92]
  [0:1] main+0x96  [0x646026]
  [0:2] __libc_start_main+0xf0  [0x7fb7ea2fc830]
  [0:3] _ZNSt8ios_base4InitD1Ev+0x52  [0x59ed7a]
Charm++ fatal error:
FATAL ERROR: No simulation config file specified on command line.

[0] Stack Traceback:
  [0:0] _Z8NAMD_diePKc+0x72  [0x640c92]
  [0:1] main+0x96  [0x646026]
  [0:2] __libc_start_main+0xf0  [0x7fb7ea2fc830]
  [0:3] _ZNSt8ios_base4InitD1Ev+0x52  [0x59ed7a]
Aborted (core dumped)

Answer 1

自从你在我回答了你的第一个问题后请我帮忙，我就尽可能多地给你启发，而没有具体的NAMD或理论生物物理学的经验。

正如在要求中所述，要运行NAMD，您需要提供一个配置文件

一旦您编写了配置文件，您就可以在运行NAMD时指定它了。配置文件是您必须根据文档编写的文本文件(我希望您知道如何这样做，或者可以从同事那里得到帮助)。您可以使用任何文本编辑器来编写文件，例如gedit。一旦编写完它，就可以使用文件的路径将其指定给NAMD。如果您将该文件命名为config，并且您当前位于保存该文件的同一目录中，则可以键入：

namd2 config

如果config文件位于名为/home/nikoot/Documents/NAMD的目录中，则可以键入：

namd2 ~/Documents/NAMD/config

我假设namd2二进制文件在您的$PATH中，因为您在问题中得到了错误！