Fwd: [gmx-users] Hen egg white lysozyme.
Viswanadham Sridhara
muta.mestri at gmail.com
Wed Aug 16 04:53:32 CEST 2006
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:
; 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> 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>>
> > 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>>
> >
> > 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>> 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 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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