Hi Ran, 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
Select group for least squares fit and RMSD calculation: Group 0 ( System) has 51129 elements Group 1 ( AMB) has 312 elements Group 2 ( SOL) has 50817 elements Group 3 ( r_1) has 78 elements Group 4 ( r_2) has 78 elements Group 5 ( r_3) has 78 elements Group 6 ( r_4) has 78 elements then I tried g_clustsize -f md_water_300.trr -mol -n index.ndx -cut 0.7 -s md_water_300.tpr (0.7 nm is the average distance between mass centers of each monomer) but I have the following message trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Reading file md_water_300.tpr, VERSION 3.3.1 (single precision) Reading file md_water_300.tpr, VERSION 3.3.1 (single precision) Using molecules rather than atoms. Not reading index file index.ndx and then, the program read the fragments of trajectory file but finish with an error Last frame 120 time 6000.000 cmid: 1, cmax: 1, max_size: 17032 ------------------------------------------------------- Program g_clustsize, VERSION 3.3.1 Source code file: matio.c, line: 532 Fatal error: Lo: 0.000000, Mid: 1.000000, Hi: 1.000000 ------------------------------------------------------- "She's a Good Sheila Bruce" (Monty Python) 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? thanks ROGELIO HERNANDEZ --- El jue 14-ago-08, Ran Friedman <[EMAIL PROTECTED]> escribió: De:: Ran Friedman <[EMAIL PROTECTED]> Asunto: Re: [gmx-users] about size of group of monomers vs time A: [EMAIL PROTECTED], "Discussion list for GROMACS users" <[email protected]> Fecha: jueves, 14 agosto, 2008, 1:55 am Hi, check out g_clustsize Ran. Rogelio Hernández wrote: Hi users I am modeling the aggregation of an amphoteric molecule in aqueous media, and to analyze the trajectories, 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 Is there any program in Gromacs to do this? thanks in advance ROGELIO HERNANDEZ __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.yahoo.com.mx/
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