[gmx-users] RMSD

[David van der Spoel]

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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> 
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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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