#langevin on # Langevin is a temperature bath method #restartfreq 10 # how often to save a restart file #restartname alanin.restart # restart file name Stepspercycle 3 # a cycle is how many steps before some thermo checking is doneĭcdfile alanin.dcd # what the output DCD is calledĭcdfreq 20 # how often to print out DCD (20 steps) Outputname output # what is the output base name Parameters alanin.params # this is normally the standard topology (top_all27.).Įxclude scaled1-4 # what forces to exclude Structure alanin.psf # absolute path (this means alanin.psf is in the working directory) Numsteps 10000 # total number of above steps Timestep 0.5 # 0.5 fs this is usually 0.2 or even 0.1 fs Note that NAMD ignores everything after a hash “#” sign. Comments have been added to describe what each line does (when it isn’t obvious). Here is a sample from the Alanine test case. There is a VMD extension ( Graphical Interface ) which can help you generate a working NAMD configuration file.
Namd alchemistry tutorial how to#
Basically, the configuration file tells the namd program how to run the simulation, what parameters to use, and the location of the other required files (input and output). A topology file (contained within both the VMD and NAMD packages)Ī description of the NAMD configuration file is HERE.A configuration file (any suffix, but ".nam" or ".conf" are commonly used).Aside from your NAMD program folder/files, you need:.If you choose to run through this NAMD tutorial, you only need to go through the “Basics of NAMD” sections. Files for the alanine test case are HERE. This is probably the best way to run it in order to minimize tkcon-like issues. You need to run NAMD from a terminal window, or you can run it directly from VMD. There is a NAMD tutorial for OS X/linux/Unix HERE.
Namd alchemistry tutorial install#
Follow the install directions enclosed in the download ( README.txt ), or look here (NAMD wiki).
We need this latest version to use QwikMD ). If you haven’t done so already, download and install the newest version of NAMD (currently 2.13. If you haven’t done so already, you will install the program, familiarize yourself with the required files, and run a test case. In this exercise, we will learn the basics of running NAMD molecular dynamics simulations.
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