[gmx-users] RMSD

[Dhananjay]

The starting structure is a homology model.
(If you need some more details then please tell me)

force field :  GROMOS96 43a1

I have not at all added or removed any ion manually.

amount of water : using  genboc -cs ( spc216.gro ) water is added.
 Here the details are as follows

Reading solute configuration
ecol
Containing 1791 atoms in 175 residues
Initialising van der waals distances...
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 4x4x5 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 17280 residues
Calculating Overlap...
box_margin = 0.315
Removed 13368 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
System total charge: 0.000
Neighborsearching with a cut-off of 0.48
Grid: 28 x 23 x 36 cells
Succesfully made neighbourlist
nri = 75512, nrj = 2292910
Checking Protein-Solvent overlap: tested 36365 pairs, removed 2592 atoms.
Checking Solvent-Solvent overlap: tested 377819 pairs, removed 4773 atoms.
Added 10369 molecules
Generated solvent containing 31107 atoms in 10369 residues
Writing generated configuration to ecolinusG_b4em.gro
ecol

Output configuration contains 32898 atoms in 10544 residues
Volume                 :     341.479 (nm^3)
Density                :     1005.02 (g/l)
Number of SOL molecules:  10369








On 8/21/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Dhananjay wrote:
> > Hello all,
> >
> > I am running mdrun for a system of protein having 182 residues. (Before
> > going for MD,  mdrun for   EM and PR  has been done as per the
> > instructions given in the online manual.)
> >  After 3ns job is over, I calculated RMSD and it is about 0.6 nm.  This
> > is too high.
> >
> > In the mailing list, most of the search suggests that RMSD  may be high
> > depends on the system.
> > One of the mails suggests to calculate RMSD domainwise. Hence I have
> > calculated it domainwise as the system consists of two domains. I found
> > that one of the domains has RMSD about 0.35 nm but the other domain is
> > still showing around 0.6 nm
>
> please give more details,
> amount of water,
> force field,
> ions
> where does that starting structure come from
> etc.
>
> >
> > Is there something  wrong in assigning the parameter ?
> >
> > Please give me suggestions.........
> >
> > Thanking you in advance.
> >
> > The full mdrun paramitors are as follows:
> >
> > title               =  xyz
> > cpp                 =  /usr/bin/cpp
> > constraints         =  all-bonds
> > integrator          =  md
> > dt                  =  0.001    ; ps !
> > nsteps              =  20000000 ; total 20 ns
> > nstcomm             =  1
> > nstxout             =  500
> > nstvout             =  1000
> > nstfout             =  0
> > nstlist             =  10
> > nstlog              =  10
> > nstenergy           =  10
> > ns_type             =  grid
> > rlist               =  0.9      ; nm
> > coulombtype         =  PME
> > rcoulomb            =  0.9      ; nm
> > rvdw                =  1.4
> > 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 three groups
> > Tcoupl              =  berendsen
> > tau_t               =  0.1      0.1
> > tc_grps             =  protein  sol
> > ref_t               =  300      300
> > ; Pressure coupling is on
> > Pcoupl              =  berendsen
> > pcoupltype          =  isotropic
> > tau_p               =  0.5
> > compressibility     =  4.5e-5
> > ref_p               =  1.0
> > ; Generate velocites is on at 300 K.
> > gen_vel             =  yes
> > gen_temp            =  300.0
> > gen_seed            =  173529
> >
> >
> > --
> > Dhananjay
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
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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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-- 
Dhananjay
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