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
<<attachment: Anamika_rmsd.jpg>>
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