Dear VMD & NAMD users,
I am new to these two platforms, interested to work on protein physics. I have installed VMD (version 1.9.4a12) on my Ubuntu 16.04 machine,
How to install NAMD on Ubuntu 16.04 ?
Thank you so much in advance !
First of all, its better to update your Ubuntu to latest one and also use latest version of NAMD. As we need C & C++ compilers to build NAMD binary source code, first use these cmds:
i) sudo apt-get install gcc
ii) sudo apt-get install g++
iii) sudo apt-get install csh
iv) sudo apt-get install tcsh
After this,
1. download the NAMD's tar file from http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD after knowing your system(being sure if the OS you are using is 64 or 32 bit as well as if CUDA is available or not, AMD/Intel Graphics have no CUDA acceptance).
2. Extract the file and go to the folder where files are extracted.
3. Open the terminal from that folder
4. then type
sudo cp namd2 /usr/local/bin/namd2
Done!!!
Follow this link: http://dharmendralinuxdiary.blogspot.com/2011/04/how-to-install-namd-in-linux.html
https://www.ks.uiuc.edu/Research/namd/2.9/ug/
Hi Chetanath,
I would look at Vijayan's post. Also, if you are lucky, which I have found happens more often than not in this case, the precompiled binaries work fine if downloaded for the appropriate configuration. Only one or two times I can think of did I need to compile NAMD for the specific setup. Its really just a matter of decompressing the NAMD executables into a folder you will reference in your job script. For example, in the following job script I actually used at one point for NAMD using CUDA acceleration on compute server namd was installed in a directory named "NAMD" in my home directory. My NAMD CUDA libraries were in "/home/tcomollo/NAMD/NAMD_2.10_Linux-x86_64-multicore-CUDA/" . charmrun and namd2 were in "/home/tcomollo/NAMD/NAMD_2.10_Linux-x86_64-multicore-CUDA/" and the .conf file was in the job folder I was launching the script from.
The "&" causes it to run in the background, so it will run even if you close the terminal window you launched it form.
"devices 0,1" uses the first two CUDA devices.
####
#!/bin/bash
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/tcomollo/NAMD/NAMD_2.10_Linux-x86_64-multicore-CUDA/
/home/tcomollo/NAMD/NAMD_2.10_Linux-x86_64-multicore-CUDA/charmrun +p18 /home/tcomollo/NAMD/NAMD_2.10_Linux-x86_64-multicore-CUDA/namd2 +idlepoll +devices 0,1 namd_npgt_prod.conf >>namd_log1.txt&
###
So the point is you can be a little creative with where you install NAMD as long as you account for it later and, if you have the appropriate file, installing is just a matter of unzipping the file. Hope this helped.
Tom
First of all, its better to update your Ubuntu to latest one and also use latest version of NAMD. As we need C & C++ compilers to build NAMD binary source code, first use these cmds:
i) sudo apt-get install gcc
ii) sudo apt-get install g++
iii) sudo apt-get install csh
iv) sudo apt-get install tcsh
After this,
1. download the NAMD's tar file from http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD after knowing your system(being sure if the OS you are using is 64 or 32 bit as well as if CUDA is available or not, AMD/Intel Graphics have no CUDA acceptance).
2. Extract the file and go to the folder where files are extracted.
3. Open the terminal from that folder
4. then type
sudo cp namd2 /usr/local/bin/namd2
Done!!!
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