Hi Justin, Thank you very much for your suggestions. I will use constraint force to force a peptide into a membrane with pulling for longer time.
yes with "POSRES_LIPID" i am keeping the lipids rigid while pulling the peptide inside. Should the lipids be flexible while pulling?? I am using pull_geometry = direction, In the tutorial mdp file you had commented saying cant get PMF with direction. So please can I know if this error of not getting PMF with direction fixed or with pull_geometry = distance will i be able to pull the peptide into membrane with still using pull direction pull_vec1 = 0.0 0.0 -1.0 Kind regards, chetan ________________________________________ From: [email protected] [[email protected]] On Behalf Of Justin A. Lemkul [[email protected]] Sent: 09 February 2011 16:40 To: Discussion list for GROMACS users Subject: Re: [gmx-users] pull code Poojari, Chetan wrote: > Hi, > > I am using umbrella sampling to pull my peptide (peptide starting from above > the lipid bilayer) into the hydrophobic core of the lipid bilayer. > > Following are my inputs i have used: > > title = Umbrella pulling simulation > define = -DPOSRES_LIPID > ; Run parameters > integrator = md > dt = 0.002 > tinit = 0 > nsteps = 250000 ; 500 ps > nstcomm = 1 > . > . > ; Pull code > pull = umbrella > pull_geometry = direction > pull_dim = N N Y > pull_start = yes ; define initial COM distance > 0 > pull_ngroups = 1 > pull_group0 = POPC > pull_group1 = Protein > pull_vec1 = 0.0 0.0 -1.0 > pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns > pull_k1 = 1000 ; kJ mol^-1 nm^-2 > > > After running the this step: grompp -f md_pull.mdp -c npt.gro -p topol.top > -n index.ndx -t npt.cpt -o pull.tpr > > i get grompp output as such: > > Pull group natoms pbc atom distance at start reference at t=0 > 0 6656 3433 > 1 105 53 -4.132 -4.132 > > I am starting to pull my peptide from 1nm above the upper leaf headgroup. I > am using POPC lipids and distance between 2 adjacent headgroups seem to be > around 4.2 nm. > > I want the peptide to be pulled into the bilayer till the lower leaf lipid > headgroups, but the peptide is being pulled only till middle of the > hydrophobic core of the bilayer. > > Please can I know what might be the problem ????? > Either you're (1) not pulling for sufficient time, (2) not pulling hard enough, or (3) the physical properties of the system don't allow for such a position. For (2), using a harmonic potential to try to force a peptide into a membrane is probably not a great idea. A constraint force is probably better. For (3), what does "POSRES_LIPID" refer to? Are you keeping the lipids too rigid by doing so? > > While viewing the conf.*gro file outputed from the traj. (after extracting > the frames), i found few lipid molecules to be broken. Please can I know if > there is a way to avoid these broken structures??? Is there a possibility > that I am not able to pull the peptide into the lower leaf head group due to > these broken lipid structures????? > > Please become comfortable with the concept of periodic boundary conditions. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin > > > Any suggestions will be helpful. > > > Kind regards, > chetan. > > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://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 -- 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
