Hello, I am using g_rmsf for analysis of a protein simulation. I want to calculate the fluctuations with respect to a reference structure (using -od option). But I am encountering a problem. Please correct me if I am wrong at some place. The following two methods are giving me different results. I have defined the residues forming helices as a separate group in the index file (to exclude loops).
1. g_rmsf -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index --> I choose Protein_CA from the index file (full protein). 2. g_rmsf -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index --> I choose helix_residues_CA from the index file (excluding loops). For the same helical regions of the protein I am getting different results from these two methods. The first one shows high fluctuations as compared to the second. My guess is that it can be due to different fitting by the choice of different atoms. But I suspect that the difference between the two is quite big than to be caused by different fitting. I also repeated the same analysis by dividing the trajectory into two parts and comparing the fluctuations with each other and the for the complete trajectory. The output in this case from the first method was consistent. Same regions were showing similar fluctuations. But for the second method the chunked parts of the trajectory displayed very small movement in certain regions where the complete trajectory analysis exhibited high fluctuations. How can this be inconsistent for the same fitting. Let me know if I am doing a mistake. Thanks. Vivek Modi Graduate Student, IITK. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
