Hello all,<br>
<br>
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.) <br>
After 3ns job is over, I calculated RMSD and it is about 0.6 nm. This is too high. <br>
<br>
In the mailing list, most of the search suggests that RMSD may be high depends on the system. <br>
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<br>
<br>
Is there something wrong in assigning the parameter ?<br>
<br>
Please give me suggestions.........<br>
<br>
Thanking you in advance.<br>
<br>
The full mdrun paramitors are as follows:<br>
<br>
title = xyz<br>
cpp = /usr/bin/cpp<br>
constraints = all-bonds<br>
integrator = md<br>
dt
= 0.001 ; ps !<br>
nsteps = 20000000 ; total 20 ns<br>
nstcomm = 1<br>
nstxout = 500<br>
nstvout = 1000<br>
nstfout = 0<br>
nstlist = 10<br>
nstlog = 10<br>
nstenergy = 10<br>
ns_type = grid<br>
rlist
= 0.9 ; nm<br>
coulombtype = PME<br>
rcoulomb = 0.9 ; nm<br>
rvdw = 1.4<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
; Berendsen temperature coupling is on in three groups<br>
Tcoupl = berendsen<br>
tau_t
= 0.1 0.1<br>
tc_grps = protein sol<br>
ref_t
= 300 300<br>
; Pressure coupling is on<br>
Pcoupl = berendsen<br>
pcoupltype = isotropic<br>
tau_p = 0.5<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br clear="all"><br>--<br>
Dhananjay<br>