Fwd: [gmx-users] Hen egg white lysozyme.
David van der Spoel
spoel at xray.bmc.uu.se
Wed Aug 16 09:30:21 CEST 2006
Viswanadham Sridhara wrote:
> Hello Dr.Spoel and others,
> There is one more problem with the simulation of hen egg white lysozyme
> simulation in water I am running. The timestep I could use is just 0.5
> fs or 0.0005ps. Is there any way around to increase the timestep.
> This is how a part of my mdp file looks like:
use constraints. please read the manual, chapters 1 and 3.
>
> ; RUN CONTROL PARAMETERS =
> integrator = md
> ;emstep = 0.001
> ;emtol = 100
> ; start time and timestep in ps =
> tinit = 0.0
> dt = 0.0005
> nsteps = 2000000
> ; number of steps for center of mass motion removal =
> comm_mode = Angular
> nstcomm = 1
> comm_grps = Protein_A
>
> ; This selects the subset of atoms for the xtc file. You can =
> ; select multiple groups. By default all atoms will be written. =
> xtc-grps =
> ; Selection of energy groups =
> energygrps = Protein_A SOL Na Cl
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; Temperature coupling =
> tcoupl = Berendsen
> ; Groups to couple separately =
> tc-grps = Protein_A SOL Na Cl
> ; Time constant (ps) and reference temperature (K) =
> tau_t = 0.1 0.1 0.1 0.1
> ref_t = 328 328 328 328
> ; Pressure coupling =
> Pcoupl = Berendsen
> Pcoupltype = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p = 1.0
> compressibility = 5e-5
> ref_p = 1.0
>
> ; SIMULATED ANNEALING CONTROL =
> annealing = no no no no
> ; Time at which temperature should be zero (ps) =
> ;zero_temp_time = 0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel = yes
> gen_temp = 328
> gen_seed = 473529
>
> ; OPTIONS FOR BONDS =
> constraints = none
> ; Type of constraint algorithm =
> constraint_algorithm = SHAKE
> ; Do not constrain the start configuration =
> unconstrained_start = no
> ; Relative tolerance of shake =
> shake_tol = 0.00001
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs_order = 4
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs_warnangle = 30
> ; Convert harmonic bonds to morse potentials =
> morse = no
>
> ; NMR refinement stuff =
> ; Distance restraints type: No, Simple or Ensemble =
> disre = No
> ; Force weighting of pairs in one distance restraint: Equal or
> Conservative =
> disre_weighting = Equal
> ; Use sqrt of the time averaged times the instantaneous violation =
> disre_mixed = no
> disre_fc = 1000
> disre_tau = 1.25
> ; Output frequency for pair distances to energy file =
> nstdisreout = 100
>
> ; Free energy control stuff =
> free_energy = no
> init_lambda = 0
> delta_lambda = 0
> sc-alpha = 0
> sc-sigma = 0.3
>
> Thanks,
> -Vissu.
>
> On 8/11/06, *David van der Spoel* <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> Viswanadham Sridhara wrote:
> > Hello everyone,
> > I could figure out that parameters for NAG are not that
> important. So, I
> > used free HEWL.
> > I started running it, but I realize that the protein started to
> rotate
> > around the center of mass with a frequency of around 200ps.
> > I used "Linear" as an option for comm_mode and I used "Protein" in
> > comm_grps.
> > Any reason Why the protein is rotating around its center of mass,
> is it
> > normal?
>
> yes.
>
> comm_mode = angular
>
> > Thanks in advance.
> > -Vissu.
> >
> > ---------- Forwarded message ----------
> > From: *David Mobley* < dmobley at gmail.com
> <mailto:dmobley at gmail.com> <mailto:dmobley at gmail.com
> <mailto:dmobley at gmail.com>>>
> > Date: Aug 8, 2006 12:32 AM
> > Subject: Re: [gmx-users] Hen egg white lysozyme.
> > To: Discussion list for GROMACS users < gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>>
> >
> > Vissu,
> >
> > Depends on what you are trying to do. Many proteins deposited in the
> > pdb contain "uninteresting" ligands bound to them (i.e. cosolvent
> > molecules, etc.) On the other hand, sometimes ligands are
> functionally
> > important or significantly affect the structure. You have to decide
> > whether you want to include NAG or not; it might help to first figure
> > out what it is and what it's used for (perhaps look up its name, and
> > look at the paper and PDB headers...).
> >
> > It is obviously harder to come up with parameters for NAG than
> not. If
> > you end up deciding it's not important, you can, for example, just
> > remove the HETATM entries dealing with it before running pdb2gmx.
> >
> > David
> >
> >
> > On 8/7/06, Viswanadham Sridhara < muta.mestri at gmail.com
> <mailto:muta.mestri at gmail.com>
> > <mailto:muta.mestri at gmail.com <mailto:muta.mestri at gmail.com>>> wrote:
> > > Hi Everyone,
> > > I am trying to simulate a protein and I am getting the
> following error
> > > message.
> > > "NAG" not found in residue topology database. I checked gmx-users
> > discussion
> > > list to find out if someone ever used 1HEW.pdb . Its a hen
> egg-white
> > > lysozyme. I did not get even a single archive about this.
> > > It is under HETATM section of .pdb file. Any help is appreciated.
> > > I know that I have to add this residue in aminoacids.dat file
> and create
> > > atoms and bonds in .rtp section. Is there any other way around?
> > > Thanks in advance,
> > > -Vissu
> > >
> > > --
> > > Viswanadham Sridhara,
> > > Graduate Research Assistant,
> > > Old Dominion University,
> > > Norfolk, VA-23529.
> > > _______________________________________________
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> >
> > --
> > Viswanadham Sridhara,
> > Research Assistant,
> > Old Dominion University,
> > Norfolk, Va-23529.
> >
> >
> >
> ------------------------------------------------------------------------
> >
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
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>
>
>
> --
> Viswanadham Sridhara,
> Research Assistant,
> Old Dominion University,
> Norfolk, Va-23529.
>
>
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>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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