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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