Dear Justin My final .xtc rmsd graph starts about 4 nm and after some steps it falls down to 0.3 and quickly goes up again, totally it is tossing around a straight line near 4 nm, what did I do wrong? As mentioned in my previous mail about centering of protein inside the box, the gro file was attached. The rmsd graph and gro files are uploaded at the following links:
gro link: https://www.hightail.com/download/elNKUXVzTkw1bmo1SE1UQw xvg link: https://www.hightail.com/download/elNKUXVzTkxtMEpYd3NUQw ***************************** I run nvt for 50000 and npt for 50000 then mdrun for 5ns the md.mdp file is title = Protein-ligand complex MD simulation ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 * 5000000 = 1000 ps (10 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = Protein LIG ; Bond parameters continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation vdwtype = switch rvdw_switch = 0.8 fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_MG_LIG Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.4e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ********************************* Sincerely M.Javaheri On Sat, 02/01/2014 04:17 AM, Justin Lemkul <jalem...@vt.edu> wrote: > On 1/31/14, 11:53 AM, Mostafa Javaheri wrote: > > Dear Justin > > > > I have a problem with centering the hetrodimer protein in the dodecahedron > > or > > octahedron box, the related commands are: > > > > 1.pdb2gmx -f A1CBIII-W3.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb > > -nochargegrp -merge all -posrefc 1000 -renum > > > > 2.editconf -f conf.pdb -o boxed.pdb -c -d 1.0 -bt dodecahedron > > > > 3.genbox -cs -cp boxed.pdb -o solvated.pdb -p topol.top > > > > in the solvated.pdb output file protein represents at the corner of the box > > and > > some of it is out of box although it will not happen for -bt cubic (whole > > protein will be centered in the box), considering periodic boundary > > condition, > > mdrun will be ok; after five ns mdrun one of the protein's chain represents > > inside the box and the other chain out of the box in md.gro file. After > > running > > trjcov several times with different options (including -pbc mol, atom, > > nojump, > > whole -center, -ur compact) none of them could put the whole protein in one > > unit > > cell. I would be grateful again for your help. > > Without seeing exactly what you've tried, it's rather futile to try to guess > what to suggest. Complexes are difficult to deal with. The first step > should > almost always be trjconv -pbc nojump, but further iterations may vary. See > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow > > and also be aware that you can (and should, in many cases) use custom index > groups for centering or other fitting, i.e. some residues at the > protein-protein > interface or something else that makes sense. Centering on "protein" > normally > fails in such cases, for reasons discussed repeatedly in the list archive. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- 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.
