![在 Ubuntu 16.04 中运行 NAMD](https://linux22.com/image/1056376/%E5%9C%A8%20Ubuntu%2016.04%20%E4%B8%AD%E8%BF%90%E8%A1%8C%20NAMD.png)
我想在 Ubuntu 16.04 中运行 NAMD,但遇到了以下错误。我该如何解决这个问题?
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)
答案1
由于我在回答了您的第一个问题后您要求我来帮忙解决这个问题,因此我将尽可能地阐明这一点,尽管我并没有 NAMD 或理论生物物理学的具体经验。
一旦你写好了配置文件在运行 NAMD 时指定它。配置文件是一个文本文件,您必须根据文档编写(我希望您知道如何编写或可以从同事那里获得帮助)。您可以使用任何文本编辑器来编写文件,例如 gedit。编写完成后,您可以使用文件路径将其指定给 NAMD。如果您命名了文件config
并且您当前位于保存文件的同一目录中,则可以键入:
namd2 config
如果config
文件位于名为 /home/nikoot/Documents/NAMD 的目录中,您可以输入:
namd2 ~/Documents/NAMD/config
我假设 namd2 二进制文件位于您的 $PATH 中,因为您在问题中遇到了错误!