Hi, Did u repeat your MD simulation of your docked complex ?
I also asked the similar question. Alex replied :" I would start several (5-10?) runs with different (random) starting impulse to get more reliable data." Best Shiyong On Tue, Oct 9, 2012 at 12:48 PM, Archana Sonawani <[email protected]> wrote: > Hi, > > I have simulated a protein-ligand complex for 5ns. I checked distance > between the important residues of protein and the ligand using g_dist. My > question is can the distance between the two groups decrease from the > initial distance (docked complex as starting structure for simulation). I > know it may increase or may remain same at the end of the simulation. > > for example: starting distance is 0.77nm and final distance is 0.8nm but > the intermediate course of simulation (around 3ns) it has decreased upto > 0.65. The complex shows stability after 2ns. While the SASA between the two > groups is around 6.3 nm2 throughout the simulation which is very high. > > This is very contradicting result. Is something wrong in the simulation? > > Thanks in advance. > > -- > Archana Sonawani-Jagtap > Junior Research Fellow, > Biomedical Informatics Centre, > NIRRH (ICMR), Parel > Mumbai, India. > 9960791339 > -- > 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 -- Shiyong Liu ------------------------------------------------------------------ Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 ------------------------------------------------------------------ Chinese Version: ------------------------------------------------------------------ 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 ------------------------------------------------------------------- -- 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
