Dear Justin, Thank you very much from your response. according you said I should set -cut with less than 0.7, but this doesn't answer me! for 0.6: 0.000000e+00 115 6.000000e+01 107 1.200000e+02 114 1.800000e+02 105 2.400000e+02 100 3.000000e+02 96 3.600000e+02 103 4.200000e+02 111 4.800000e+02 99
for 0.5 0.000000e+00 139 6.000000e+01 135 1.200000e+02 136 1.800000e+02 136 2.400000e+02 140 3.000000e+02 139 3.600000e+02 142 4.200000e+02 138 4.800000e+02 137 Can you help me about this, Please? Best Regards Sara > > > > > Dear Gromacs Users, > > I have several questions about g_clustsize, Please help me. > I have several micelles in my system and I want to calculate: the number of > monomers in micelles and cluster number and monomer number during the time of > simulation, I used from this command as is follows: > g_clustsize -f clustered.xtc -s c.tpr -tu us -mol -cut 0.7 -nc nclust.xvg -ac > avclust.xvg -mc maxclust.xvg > I have 150 monomer initially in my system. I selected -cut from rdf.xvg for > tail-tail that 0.7 was the first minimum in this graph. > > > > > 1- the nclust.xvg file is as follows: > @ title "Number of clusters" > @ xaxis label "Time (us)" > @ yaxis label "N" > @TYPE xy > 0.000000e+00 104 > 6.000000e+01 88 > 1.200000e+02 89 > 1.800000e+02 85 > 2.400000e+02 79 > 3.000000e+02 79 > 3.600000e+02 91 > 4.200000e+02 89 > . . . . . .. . .. . .. . .. ... . > > . . ... . .. .. .. . . .. . .. .. > > . . ... . . . . ... ............. > whereas in the first step of simulation there is no cluster and it should be > 0!!! > You've set the cutoff value to 0.7 nm, so any molecules with contacts within this distance will be considered clustered. Out of 150 monomers, some are within this distance in the starting frame. Note that with 104 clusters, the majority of your 150 monomers are basically in individual clusters. > > 2- when I choose -tu (ps, ms, us , ... ) there is no difference among them > about time either file .xvg and graphs!!!why and where is problem? This is odd. The code indicates that you should be able to display whatever units you choose. In any case, you should determine from the trajectory what the interval (in ps) is and plot accordingly. Time units can always be manipulated after the fact with simple multiplication or division operations. > 3- how should I find the number of monomers from first to end of simulation > that it should be 150 in the first step. > Probably not with g_clustsize. It does exactly the opposite, but perhaps you can back-calculate the results using a combination of output files. It's not immediately clear to me how you would do that, though. Perhaps someone else can comment. -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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists