[gmx-users] Abnormal fluctuation in RMSD

[Justin A. Lemkul]

Quoting Anamika Awasthi <aawasthi28 at gmail.com>:

>  Dear all,
>
> I am working on a biological dimer of 330 residues.
> I dont think that I got any error message when I did grompp.

Don't think, or don't know?  These types of things are important.

> Please find pr.mdp filesbelow and RMSD as attachment.
> Please tell me why it happened?

Well, look at your trajectory - what's happening when the RMSD graph spikes? 
That should provide you with some ideas.  My guess would be your protein is
jumping across the simulation box, but you have not described your setup - box
size/distance from protein to the box edge, and whether or not you observed any
periodic jumping.

-Justin

>
> pr.mdp
> ;
> ;       User spoel (236)
> ;       Wed Nov  3 17:12:44 1993
> ;       Input file
> title               =   CM_2ao2_A
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.001
> nsteps              =  100000
> nstcomm             =  1
> nstxout             =  250
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1
> coulombtype         =  PME
> rcoulomb            =  1.0
> rvdw                =  1.0
> 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
> Tcoupl              = berendsen
> tau_t               = 0.01      0.01
> tc_grps             = protein   non-protein
> 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
>
>
> Thanking you
>
>  With best regards
>      Anamika
>



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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