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

--
========================================

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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