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
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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