[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

[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 t

[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

[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 extra

[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.

[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

[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-use