[gmx-users] g_clustsize

[Justin Lemkul]

On 9/27/12 2:47 PM, mohammad agha wrote:
> Dear Gromacs users
>
> I have one big problem with g_clustsize!
>
> I see 9 micelles in my system after running. When I use g_clustsize for number of clusters and average cluster size, they don't emphasize each other, and I see 9 micelles from 360000 ps to 1200000 ps in my box, but results of nclust.xvg is not regular and have very fluctuations. I examine these results in different -cut. Please see my results:
> nclust.xvg
>    9.240000e+05          11
>    9.300000e+05          11
>    9.360000e+05           9
>    9.420000e+05           7
>    9.480000e+05           5
>    9.540000e+05           6
>    9.600000e+05          16
>    9.660000e+05          13
>    9.720000e+05          13
>    9.780000e+05          12
>    9.840000e+05           9
>    9.900000e+05          12
>    9.960000e+05           7
>    1.002000e+06          13
>    1.008000e+06          10
>    1.014000e+06           5
>    1.020000e+06           8
>    1.026000e+06           4
>    1.032000e+06           5
>    1.038000e+06          10
>    1.044000e+06          10
>    1.050000e+06           8
>    1.056000e+06           9
>    1.062000e+06           8
>    1.068000e+06           5
>    1.074000e+06          12
>    1.080000e+06          11
>    1.086000e+06           8
>    1.092000e+06           8
>    1.098000e+06           9
>    1.104000e+06          10
>    1.110000e+06           8
>    1.116000e+06          10
>    1.122000e+06           8
>    1.128000e+06           4
>    1.134000e+06           5
>    1.140000e+06          10
>    1.146000e+06          10
>    1.152000e+06          11
>    1.158000e+06          10
>    1.164000e+06           7
>    1.170000e+06           6
>    1.176000e+06           4
>    1.182000e+06          14
>    1.188000e+06           8
>    1.194000e+06           2
>    1.200000e+06           6
>
> and avclust.xvg:
>
> 9.840000e+05      83.333
>    9.900000e+05      62.500
>    9.960000e+05     107.143
>    1.002000e+06      57.692
>    1.008000e+06      75.000
>    1.014000e+06     150.000
>    1.020000e+06      93.750
>    1.026000e+06     187.500
>    1.032000e+06     150.000
>    1.038000e+06      75.000
>    1.044000e+06      75.000
>    1.050000e+06      93.750
>    1.056000e+06      83.333
>    1.062000e+06      93.750
>    1.068000e+06     150.000
>    1.074000e+06      62.500
>    1.080000e+06      68.182
>    1.086000e+06      93.750
>    1.092000e+06      93.750
>    1.098000e+06      83.333
>    1.104000e+06      75.000
>    1.110000e+06      93.750
>    1.116000e+06      75.000
>    1.122000e+06      93.750
>    1.128000e+06     187.500
>    1.134000e+06     150.000
>    1.140000e+06      75.000
>    1.146000e+06      75.000
>    1.152000e+06      68.182
>    1.158000e+06      75.000
>    1.164000e+06     107.143
>    1.170000e+06     125.000
>    1.176000e+06     187.500
>    1.182000e+06      53.571
>    1.188000e+06      93.750
>    1.194000e+06     375.000
>    1.200000e+06     125.000
> Whereas the size of clusters in the box are similar when I see with ngmx. I don't know where is my problem!!!
>

I don't see anything that indicates a problem.  Your average over the snippet of 
nclust.xvg is 8.7, which is consistent with your observations.  I don't 
understand what the complaint is about the data in avclust.xvg.

-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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