Re: [gmx-users] what factors effetc the simulation during energy minimization
bhargavi ch wrote: hi.. the sudden shoot up was observed in the RMS because of molecule breakage into monomer and dimer.we have also mutated some surface hydrophobic aminoacid and dint observe shoot up in any of the mutation. We have also observed the same shoot in the case of X ray crystallographic structure of template protein, when we did 10 ps simulation. what are the parameters which we need to take to avoid such shoot up?? As Mark pointed out, based on your original description, you are probably seeing PBC effects. Use trjconv to remove periodicity, and analyze the RMSD again. -Justin thanx Bhargavi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] what factors effetc the simulation during energy minimization
hi.. the sudden shoot up was observed in the RMS because of molecule breakage into monomer and dimer.we have also mutated some surface hydrophobic aminoacid and dint observe shoot up in any of the mutation. We have also observed the same shoot in the case of X ray crystallographic structure of template protein, when we did 10 ps simulation. what are the parameters which we need to take to avoid such shoot up?? thanx Bhargavi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] what factors effetc the simulation during energy minimization
bhargavi ch wrote: hi.. I have been doing the simulation of protein which has 3 chains (trimer)and each chain with a length of 80 amino acids. I have done the simulation for 5ns. I have observed a sudden peak at 4ns so i continued simulating it to 10ns ..the peak which started at 4ns extended till 8ns .i have extracted the pdbs at this particular time frames.i found that the trimer is been spilt into monomer and dimer.i wanted to know exactly what are the parameters i need to adjust during the simulation to get a stabilised modelled structure. Energy minimization does not occur over time, so you are mis-describing something here. You haven't told us what you're observing to peak at 4ns. Perhaps you need to understand some material here http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] what factors effetc the simulation during energy minimization
hi.. I have been doing the simulation of protein which has 3 chains (trimer)and each chain with a length of 80 amino acids. I have done the simulation for 5ns. I have observed a sudden peak at 4ns so i continued simulating it to 10ns ..the peak which started at 4ns extended till 8ns .i have extracted the pdbs at this particular time frames.i found that the trimer is been spilt into monomer and dimer.i wanted to know exactly what are the parameters i need to adjust during the simulation to get a stabilised modelled structure. thanx Bhargavi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
