Re: [gmx-users] RMSF: Different results for same residue
Il 15/04/2011 18:45, Alok Jain ha scritto: Hi, I am simulating a tetrameric protein in membrane. The simulation is for 30ns. I wish to calculate RMSF for just one monomer (A). I thought of doing this in two ways, 1. I input the residue numbers for the monomer A by creating an index.ndx file to calculate RMSF only for the selected monomer CA atoms. g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx 2. I calculate RMSF for the complete protein CA atoms g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg I find the output from these to commands for the same monomer A residues are different. The second command calculates a very high RMSF for the same residues. Why is it so ?? Or am I making a mistake at some place ?? Thanks in advance. Alok The reason is that in the two cases you used two different groups to fit the protein. Different fit generates different result. If you try to calculate RMSF, fitting on the subunit B, you will find a third result. I guess the subunit B should fluctuate less than case 2) -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RMSF: Different results for same residue
Alok Jain wrote: Hi, I am simulating a tetrameric protein in membrane. The simulation is for 30ns. I wish to calculate RMSF for just one monomer (A). I thought of doing this in two ways, 1. I input the residue numbers for the monomer A by creating an index.ndx file to calculate RMSF only for the selected monomer CA atoms. g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx 2. I calculate RMSF for the complete protein CA atoms g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg I find the output from these to commands for the same monomer A residues are different. The second command calculates a very high RMSF for the same residues. Why is it so ?? Or am I making a mistake at some place ?? The selected index group has a least-squares fit performed on it. If the fitting group is different, the output RMSF will be different. In case (1) you're doing the fitting and establishing a reference for RMSF from just one monomer and then doing the calculation on that group. In case (2) you're using the whole protein for the calculation. -Justin Thanks in advance. Alok -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RMSF: Different results for same residue
Hi, I am simulating a tetrameric protein in membrane. The simulation is for 30ns. I wish to calculate RMSF for just one monomer (A). I thought of doing this in two ways, 1. I input the residue numbers for the monomer A by creating an index.ndx file to calculate RMSF only for the selected monomer CA atoms. g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg -n index.ndx 2. I calculate RMSF for the complete protein CA atoms g_rmsf -f *.xtc -s *.tpr -od rmsdev.xvg I find the output from these to commands for the same monomer A residues are different. The second command calculates a very high RMSF for the same residues. Why is it so ?? Or am I making a mistake at some place ?? Thanks in advance. Alok -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
