[gmx-users] Abnormal fluctuation in RMSD

[Florian Haberl]

Hi,

On Friday, 15. February 2008 14:51, Anamika Awasthi wrote:
>  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.
> Please find pr.mdp filesbelow and RMSD as attachment.
> Please tell me why it happened?
>
> 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

you are using PBC and your system is sometimes jumping out of the box, so you 
have to mirror it back to its normal box


trjconv -f yourtraj.trr -o yourtraj_fit.trr -s topol.tpr -pbc nojump

should fix it again.


Greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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