On Sun, Apr 7, 2013 at 11:17 AM, Albert <[email protected]> wrote:
> On 04/06/2013 08:52 PM, Justin Lemkul wrote: > >> Hard to tell. Does your ligand have a suitable exit pathway exactly >> aligned >> along the x-axis? Have you tried increasing the pull rate? How long is the >> simulation? I don't even see nsteps in the above .mdp file. How about >> increasing the force constant? Is the vector connecting the COM of the >> entire protein and the COM of the ligand suitable for describing the exit >> pathway? >> >> -Justin >> > > Hello Justin: > > thanks a lot for kind rely. > Yes, I adjust the conformation of whole protein/ligand so that it can > exist from X-axies. I only show part of the .mdp file so some of then are > not shown. > > > ; Run parameters > integrator = md > dt = 0.002 > tinit = 0 > nsteps = 500000 ; 500 ps > nstcomm = 10 > ; Output parameters > nstxout = 5000 ; every 10 ps > nstvout = 5000 > nstfout = 1000 > nstxtcout = 1000 ; every 1 ps > nstenergy = 1000 > > > probably I should consider use part of the protein such as residues around > binding pocket as COM for protein instead of whole protein? I applied for > 1ns with rate pull_rate1= 0.001, so at then end of pulling, the distance > for COMprotein and COM ligand should be 10A. Probably this is too short for > whole protein as COM? > > Let me clear one thing up first. 1 ns of pulling with a 0.001 nm/ps pull rate will not necessarily cause the ligand to be displaced by 1 nm. The particle pulling the virtual spring will be displaced by 1 nm, but the ligand will only move as a function of this applied force and the restoring forces (i.e. interactions between the ligand and protein). Choosing a more suitable reference group and running the simulation for longer will produce the desired result. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
