<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi Ran, <br><br>I tried to use g_clustsize as you suggest me but I had problems, for example in the case of a simulation where I put 4 monomers inside water box I did an index that contain the following groups<br><br>Select group for least squares fit and RMSD calculation:<br>Group 0 ( System) has 51129 elements<br>Group 1 ( AMB) has 312 elements<br>Group 2 ( SOL) has 50817 elements<br>Group 3 ( r_1) has 78 elements<br>Group 4 ( r_2) has 78
elements<br>Group 5 ( r_3) has 78 elements<br>Group 6 ( r_4) has 78 elements<br> <br>then I tried <br><br>g_clustsize -f md_water_300.trr -mol -n index.ndx -cut 0.7 -s md_water_300.tpr<br><br>(0.7 nm is the average distance between mass centers of each monomer) <br><br> but I have the following message<br><br><span style="font-weight: bold;">trn version: GMX_trn_file (single precision)</span><br style="font-weight: bold;"><span style="font-weight: bold;">Reading frame 0 time 0.000 Reading file md_water_300.tpr, VERSION 3.3.1 (single precision)</span><br style="font-weight: bold;"><span style="font-weight: bold;">Reading file md_water_300.tpr, VERSION 3.3.1 (single precision)</span><br
style="font-weight: bold;"><span style="font-weight: bold;">Using molecules rather than atoms. Not reading index file index.ndx</span><br><br>and then, the program read the fragments of trajectory file but finish with an error<br><br><span style="font-weight: bold;">Last frame 120 time 6000.000 </span><br style="font-weight: bold;"><span style="font-weight: bold;">cmid: 1, cmax: 1, max_size: 17032</span><br style="font-weight: bold;"><span style="font-weight: bold;">-------------------------------------------------------</span><br style="font-weight: bold;"><span style="font-weight: bold;">Program g_clustsize, VERSION 3.3.1</span><br style="font-weight: bold;"><span style="font-weight: bold;">Source code file: matio.c, line: 532</span><br style="font-weight: bold;"><br style="font-weight: bold;"><span style="font-weight: bold;">Fatal error:</span><br style="font-weight: bold;"><span
style="font-weight: bold;">Lo: 0.000000, Mid: 1.000000, Hi: 1.000000</span><br style="font-weight: bold;"><br style="font-weight: bold;"><span style="font-weight: bold;">-------------------------------------------------------</span><br style="font-weight: bold;"><br style="font-weight: bold;"><span style="font-weight: bold;">"She's a Good Sheila Bruce" (Monty Python)</span><br><br><br>do you know what is my error?? my other question is about group that i should select (AMB is the group that contain 4 monomers) or should i need select one of the groups that contain only one monomer?<br><br>thanks<br><br>ROGELIO HERNANDEZ<br><br>--- El <b>jue 14-ago-08, Ran Friedman <i><r.friedman@bioc.uzh.ch></i></b> escribió:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">De:: Ran Friedman <r.friedman@bioc.uzh.ch><br>Asunto: Re: [gmx-users] about size of group of monomers vs time<br>A:
rahl_emc@yahoo.com.mx, "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Fecha: jueves, 14 agosto, 2008, 1:55 am<br><br><div id="yiv443869561">
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Hi,<br>
<br>
check out g_clustsize<br>
<br>
Ran.<br>
<br>
Rogelio Hernández wrote:
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<pre><tt><tt>Hi users<br><br>I am modeling the aggregation of an amphoteric molecule in aqueous media, and to analyze the trajectories, <br>I want to plot the number of monomers in the aggregates vs time and the kind of groups because in some trajectories i have dimers and monomers, or dimers and trimers and so on<br><br>Is there any program in Gromacs to do this?</tt></tt><br> </pre>
thanks in advance<br>
<br>
ROGELIO HERNANDEZ<br>
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</div></blockquote></td></tr></table><br>__________________________________________________<br>Correo Yahoo!<br>Espacio para todos tus mensajes, antivirus y antispam ¡gratis! <br>Regístrate ya - http://correo.yahoo.com.mx/