RDF calculation with NAMD

From: Dian Jiao (oscarjiao_at_gmail.com)
Date: Tue Jan 14 2014 - 15:05:32 CST

I am trying to calculate the radial distribution function for some metal
ions in water (zn, cs, etc). Here is what I plan to do:

1. solvate ion in water box
2. run npt to equilibrate until volume of the water box stabilizes.
3. switch to nvt for production run.

Since I am not an expert of NAMD, I have the following technical questions:

1. for step 2, should I run several short npt (update cellBasisVector1 etc
every time) or a long npt?
2. How to plot the dimension fluctuation of the simulation box vs
simulation time?
3. For prodution run, is it better to run nvt or npt?
4. what is the best way to calculate rdf? Is there any script available?


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