Hi Liu Shiyong, No, I didn't repeat any simulation. My intention is to compare two large compounds with our designed molecule which is comparatively smaller.
On Wed, Oct 10, 2012 at 6:01 AM, Liu Shiyong <liushiy...@gmail.com> wrote: > 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 <ask.arch...@gmail.com> > 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 gmx-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 > > > > -- > 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 gmx-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 > -- Archana Sonawani-Jagtap Junior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing list gmx-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
