[gmx-users] Abnormal fluctuation in RMSD

[Anamika Awasthi]

 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
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