Running and Verifying NAMD

Use PuTTY to log in to the server as the root user.
Run the following command to set the environment variable for the NAMD executable file:
```
export PATH=/path/to/NAMD/NAMD-2.13/build/NAMD_2.13_Source/Linux-ARM64-g++/:$PATH
```
Run the following command to go to the test case directory:
```
cd /path/to/CASE
```
Run the following command to decompress the case file:
```
tar -xf apoa1.tar.gz
```
Run the following command to modify the case file:
1. Open the test case file.
```
vi apoa1/apoa1.namd
```
2. Press i to enter the insert mode and add the following content to the end of the file:
```
FFTWEstimate yes
FFTWUseWisdom no
```
3. Press Esc, enter :wq!, and press Enter to save the file and exit.
Run the following commands to start a test:
```
cd apoa1
mpirun --allow-run-as-root --mca btl ^openib -np 1 namd2 +ppn 96 apoa1.namd +setcpuaffinity 2>&1 |tee -a namd.log
```
Check the value of days/ns in the last Info:Benchmark time in the namd.log file. A smaller value indicates better performance. You can also convert the value to the value of ns/days. A higher value indicates better performance.

Figure 1 shows an example of the test result.

Figure 1 Result example

Parent topic: NAMD 2.13 Porting Guide (CentOS 7.6)