Hi, For your ease of understanding regarding what is happening during this above said umbrella-mdrun, I have shared the trajectory video file the following link. https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
Is this normal given that the mdp code being used ? I basically have no idea with this step, so please help me out. I'm using gromacs-4.6.2. On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > > I have completed pulling as per the tutorial stated. But having a strange > issue during umbrella sampling. When I execute: > *mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf > pullf-umbrella8.xvg -px pullx-umbrella8.xvg* > The gro file generated at the end shows the ligand is way far compared to > starting position, as if another pulling is done ! > Please suggest me a way to tackle this issue. If this thing happens to all > the configurations generated during pulling then how am I supposed to get > the PMF ? > > The md_umbrella.mdp I'm using is: > title = Umbrella pulling simulation > define = -DPOSRES > ; Run parameters > integrator = md > dt = 0.002 > tinit = 0 > nsteps = 5000000 ; 10 ns > nstcomm = 10 > ; Output parameters > nstxout = 50000 ; every 100 ps > nstvout = 50000 > nstfout = 5000 > nstxtcout = 5000 ; every 10 ps > nstenergy = 5000 > ; Bond parameters > constraint_algorithm = lincs > constraints = all-bonds > continuation = yes > ; 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 > refcoord_scaling = com > ; 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_ngroups = 1 > pull_group0 = Protein_chain_A > pull_group1 = ACO > pull_geometry = direction > pull_dim = N N Y ; pulling in Z dimension > pull_rate1 = 0.0 > pull_k1 = 1000 ; kJ mol^-1 nm^-2 > pull_start = yes ; define initial COM distance > 0 > pull_vec1 = 0 0 -1 > > My question is despite the pull_rate1 being 0.0, why the ligand is moving > ? Is it the pull_start or something else I'm missing here resulting in such > a crash ? > > Your suggestions will be highly appreciated. > Thank you. > > -- > Abhisek Mondal > > *Senior Research Fellow* > > *Structural Biology and Bioinformatics Division* > *CSIR-Indian Institute of Chemical Biology* > > *Kolkata 700032* > > *INDIA* > -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.