[gmx-users] coenzyme-protein complex
Justin Lemkul
jalemkul at vt.edu
Sun Feb 2 17:12:41 CET 2014
On 2/2/14, 3:46 AM, Mostafa Javaheri wrote:
> 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
What was/were your trjconv command(s)? Clearly the protein is not correctly
re-imaged in a way that g_rms produces useful output. Visualization of the
trajectory you are processing should indicate what is going on quite clearly.
-Justin
> 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 <jalemkul at 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
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu>
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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--
==================================================
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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