[Mutinf-news] Re: Mutinf Query

[Dilraj LAMA]

Dear Chris,
           I am not sure if you received my last email. Just in case  
you have not, I am appending the content below. In case you get  
sometime to go through this mail, I will be glad to hear from you.

I wanted to get your opinion on a couple of more things.

1) I notice that in your paper, you have performed multiple short  
simulations of 10ns each. Whereas I am doing 3 long simulations of  
100ns each and then dividing it into blocks. Which of the two options  
do you think will be more advisable for the current analysis? I know  
this is a subjective term but just would like to hear about it from you.

2)I am taking all possible Chi angles calculation using "g_chi". I was  
initially restricting it to 2. I suppose we need to take all the chi  
angles rather than just 2.


Will be looking forward to your response.

Best Regards,
Dilraj.

Quoting Dilraj LAMA <dilrajl at bii.a-star.edu.sg>:

> Dear Chris,
>           I did the calculation on my simulation trajectories. Well  
> I have some queries and I will be glad if you give me your point of  
> view on the matter.
>
> 1) I have done 100ns simulation in triplicates and then divided the  
> simulation into blocks of 50ns each thereby having six blocks for  
> the analysis. Is that fine?
>
> 2) For the analysis I have used the following command:
>
> python2.6 $PATH dihedral_mutent.py -g gcc -x $PATH/mutinf_ver2.1/  
> -d/  -a yes -o 6 -w 30 -p 0 -n 6 -m 2 -c yes  
> $PATH/mutinf_ver2.1/residue.reslist > temp
>
> Are the parameters I have used fine? Especially the bin size (-w  
> 30). Are there any other parameters I need to consider?
>
> I see in the tutorial that some of the options are within quotation  
> like -a "yes". Is that critical or I can do away with the quotations?
>
> 3) After the analysis, a set of output files are generated. I have  
> just used "residue.reslist-nsims6-structs50000  
> bin30_bootstrap_avg_mutinf_res_sum_0diag.txt" which gives the mutual  
> information between residues to plot the clustered and unclustered  
> heat map plots.
>
> However, besides these a number of other files are generated. I got  
> the description of some of these files from the tutorial. But we  
> don't have the description for all the files.
>
> Are many of them intermediate files and hence not critical for the  
> final output analysis?
>
> 4)I refereed to your JCTC paper where you have made plots like that  
> for Figure 4 and Figure 5. From the example that you have mentioned  
> in the tutorial on how to make such plots, I don't get the file  
> names that you have mentioned in the tutorial in the output file  
> from my analysis.
>
> For example I don't get the output file with the following extension
> "_quarter_kT_CA_dist_matrix_fixnames.txt". Has there been some  
> modifications in the file naming with the latest version or Am I  
> missing something?
>
> Sorry for this very long email. I hope you will have the patience to  
> go through it. will be glad to get your feedback.
>
> Best regards,
> Dilraj.
>
>