I wanted to run NAMD in Ubuntu 16.04, however it encountered with the following error. How I can solve this problem?

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
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)

1 Answer

Since you asked me to help with this after I answered your first question, I am giving as much illumination as I can without specific experience of NAMD or theorectical biophysics.

As stated among the requirements to run NAMD you need to supply a configuration file

Once you've written your config file you specify it when running NAMD. The configuration file is a text file that you must write according to the documentation (I hope you know how to do this or can get help with it from colleagues). You can use any text editor to write the file, for example gedit. Once you have written it, you specify it to NAMD with the path to the file. If you named the file config and you are currently in the same directory where the file is saved, you could type:

namd2 config

if the config file is in a directory called /home/nikoot/Documents/NAMD you could type:

namd2 ~/Documents/NAMD/config

I am assuming the namd2 binary is in your $PATH since you managed to get the error in your question!

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