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 <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
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--
Dhananjay
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