[gmx-users] help

[Justin Lemkul]

On 12/2/12 2:17 AM, 申昊 wrote:
> 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)?

The dist.xvg file from g_dist has the total distance, then the x, y, and z 
components of that distance.  If you want only the total distance for analysis, 
you have to parse that yourself with a script or suitable awk command.

>       (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?

You can have negative values within the (x,y,z) portion of dist.xvg since the 
components are vectors.

ACF calculations are discussed in the manual, section 8.5.

>    [2] Does the tetrahedral order parameter of water can be calculated by g_order? How to generate this               parameter?

g_order is for lipids.

>    [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.
>

My virtual site tutorial is one example of special uses of virtual sites dealing 
solely with linear molecules.  Virtual sites can be useful in a number of 
situations.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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