[gmx-users] help

申昊 shenhao at mail.bnu.edu.cn
Sun Dec 2 08:17:41 CET 2012

Hi everyone,
  I am a new one on using gromacs. Now I have some problems.
  [1] I want using g_analyze to calculate the self-ACF with the dist.xvg resulted from g_dist, the file named        dist.xvg consists two lists of time(ns) and distance(nm), respectively.
     (a)why the result shows a combination of four curves? Is there any options missed (for plotting the only         one curve)?
     (b)I noticed that some regions of the curves were negative, is it correct? Whether the calculation of            ACFs is according to the integral methods or cosine methods?
  [2] Does the tetrahedral order parameter of water can be calculated by g_order? How to generate this               parameter? 
  [3] Virtual sites are useful in some simulations. I read the tutorial on the web site of http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/. What i really care about is whether the virtual sites should always be used for gas state. I mean, in solutions, the oscillations of the angles are rational.
   Any questions would be greatly appreciated!  Thanks.
Hao Shen

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