<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div><span><br></span></div><div><span>Dear Prof. Spoel</span></div>
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<div><span>Thank you very much for your reply, but I don't understand what I want!</span></div><div><span>In the g_clustsize there is only " -cut = Largest distance (nm) to be considered in a cluster " between my questions and I don't know the base of selection for -cut. I practice different numbers for -cut and took different results but may I know the most exact number for it? <br></span></div><div><br><span></span></div><div><span>Best Regards</span></div><div><span>Sara<br></span></div><div style="font-family: verdana, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> David van der Spoel <spoel@xray.bmc.uu.se><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight:
bold;">Sent:</span></b> Saturday, November 26, 2011 10:09 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] g_clustsize<br> </font> <br>
On 2011-11-26 18:55, mohammad agha wrote:<br>> Dear Prof.<br>><br>> I have some problems about g_clustsize program and I didn't find my<br>> answer in mailing list. Please help me.<br>> I don't know what is the base of selection for -cut option?<br>> In my system after doing g_clustsize, when I see nclust.xvg file, it<br>> looks like all the atoms in the system were used to find clusters.<br>><br>that's correct, g_clustsize -h explains it.<br><br>> @ title "Number of clusters"<br>> @ xaxis label "Time (ps)"<br>> @ yaxis label "N"<br>> @TYPE xy<br>> 0.000000e+00 413<br>> 1.500000e+02 362<br>> 3.000000e+02 348<br>> 4.500000e+02 304<br>> 6.000000e+02 274<br>> 7.500000e+02 255<br>> 9.000000e+02 243<br>> 1.050000e+03 233<br>> 1.200000e+03 218<br>> 1.350000e+03 211<br>> 1.500000e+03 199<br>> 1.650000e+03 190<br>> 1.800000e+03 192<br>> 1.950000e+03 179<br>> 2.100000e+03 172<br>>
2.250000e+03 170<br>> .....<br>> .....<br>> .....<br>> 5.992500e+05 9<br>> 5.994000e+05 10<br>> 5.995500e+05 9<br>> 5.997000e+05 9<br>> 5.998500e+05 9<br>> 6.000000e+05 9<br>> My system consist of 500 monmer.<br>><br>> Please help me.<br>><br>> Best Regards<br>> SARA<br>><br>><br>><br>><br>><br><br><br>-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br><a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> http://folding.bmc.uu.se<br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at
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