[gmx-users] factors effecting the simulation
hi.. We were working on the simulation of protein which has 3 chains (trimer) and each chain with a length of 80 amino acids. We have done the simulation for 5ns.We have observed a sudden shoot up in the RMS at 4ns so we continued simulating it to 10ns .The peak which started at 4ns extended till 8ns because of molecule breakage into monomer and dimer. we have also mutated some surface hydrophobic amino acid and dint observe shoot up in any of the mutated simulations. We have also observed the same shoot in the case of X ray crystallographic structure of template protein, when we did it for 10 ps simulation. We have done position Restraint Dynamics for 100 ps. What are the parameters i need to adjust during the simulation to get a stabilized modeled structure?? Does the PR parameters have any effect on simulation?? 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
[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
[gmx-users] (no subject)
hi.. I am working on 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 shoot up in the RMS 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
[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
[gmx-users] position restraint dynamics
Hi we are simulating a protein of 260 a.a length which is a trimer...How does the mdrun time during the position restraint dynamics affects the Full Dynamics results??? Regards 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
[gmx-users] position restraint dynamics
Hi..dear gromacs users...How do we decide the ideal time to run PR??we are simulating a protein of 260 amino acids which is a tirmer...we have done the PR for 10 ps first time and 100ps for the second ...i had observed a stable graph in the latter compared with the other...and on what factors does do we decide the time interval in PR lucky. ___ 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] PR dynamics
Hi we are simulating a protein of 260 a.a length which is a trimer...How does the MDRUN time during the PR affects the Full Dynamics results??? Lucky ___ 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
