[gmx-users] about size of group of monomers vs time

Rogelio Hernández rahl_emc at yahoo.com.mx
Thu Aug 14 17:57:20 CEST 2008

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?



--- El jue 14-ago-08, Ran Friedman <r.friedman at bioc.uzh.ch> escribió:
De:: Ran Friedman <r.friedman at bioc.uzh.ch>
Asunto: Re: [gmx-users] about size of group of monomers vs time
A: rahl_emc at yahoo.com.mx, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Fecha: jueves, 14 agosto, 2008, 1:55 am


check out g_clustsize


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





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