Dear Justin, Thank you for your reply. To be sure I carefully ran the simulations again using the following .mdp file that includes the pull lines and -DPOSRES_B to restrain chain B from being pulled when chain A is being pulled (it is the .mdp file given in the tutorial):
title = Umbrella pulling simulation define = -DPOSRES_B ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250000 ; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 I get slightly different distances but it is still now working. From the load of the trajectories chain B is not getting pulled. However, after running the distance.pl script I get a COM distance within the range 2.3nm to 6.0nm). Can you please help me to understand what I am doing wrong? My command line is: Grompp -f pull.mdp -c after_npt.gro -p topol.top -o pull.tpr -t state.cpt (checkpoint file from the previous npt step) -n index.ndx (which includes groups 19 and 20, chains A and B respectively). Mdrun then uses pull.tpr... Please don't hesitate to ask me any other information you may need to figure this out. I am not sure what I am doing wrong.. Thank you for your time. Davide On 12/12/12 2:38 AM, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 12/11/12 2:40 AM, Davide Mercadante wrote: >> Dear Justin, >> >> I have been practicing umbrella sampling simulations following your >>tutorial >> step by step. I have just finished to perform the pull simulations to >> identify the configurations to use in the umbrella runs. I have used the >> distances.pl script to run iteratively g_dist and the resulting file >> (summary_distances.dat) is showing a distance between 2.62nm (for >>conf0.gro) >> and 5.3nm (for conf500.gro). I don't seem to have the values reported >>in the >> tutorial at all (in the tutorial is reported that the COM distance >>would be >> something of an order of magnitude lowerŠ) and I am not sure if >>something is >> gone wrong. >> > >The distances shown in the tutorial are just an illustrative example and >don't >necessarily correspond to anything you might obtain. A distance of 2.62 >nm for >the initial configuration does not seem right to me though; it should be >on the >order of 0.5 nm, coincident with interpeptide spacing in the beta-sheet. > >> I have also tried to visualize the trajectories but I am not able to see >> chain_A moving away from the rest of the fibril. I have set, at the end >>of >> the topol_Protein_chain_B.itp file, the lines suggested to restrain >>chain B. >> >> #ifdef POSRES_B >> #include "posre_Protein_chain_B.itp" >> #endif >> >> I have used all the input files given in the tutorial and the >>commands/files >> extensions suggested. >> >> Can you please help me to understand if I am doing something wrong? >> > >What you're reporting is not consistent - your distances increase over >time, but >then you say peptide A does not move away from the others? That's not >possible. > If peptide A doesn't move, then the COM distance should remain >relatively >constant. Are you loading the right trajectory (i.e., the actual SMD, >not a >previous equilibration or something else)? > >-Justin > >-- >======================================== > >Justin A. Lemkul, Ph.D. >Research Scientist >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 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 -- 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? 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