[gmx-users] [Fwd: DNA separation]
Beniamino Sciacca
superbenji83 at yahoo.it
Sun May 21 23:09:15 CEST 2006
Dear community,
I've a problem during the MD of a double strand molecule of DNA.
I worked with heavy H and virtual site.
I minimized in vacuum, then i solvated and minimezed.
Later I've heated (simulated annealing) for 50 ps.
Then I simulated 1200 ps of MD.
There has not been any crash.
Viewing RMSD, in 4 point there is a peak.
Viewing, with VMD, the dinamic in the same steps the molecule is
separated in 2 molecule single strand; the next step the molecule return
in double strand configuration and the dinamic continue without any problem.
I attach .xvg and .mdp file of the dinamic.
I thank you in advance for your answer
Beniamino Sciacca
-------------- next part --------------
title = MD simulation of Hen Egg White Lysozyme
cpp = /lib/cpp
include = -I../top
define = -DFLEXIBLE
integrator = md
;Total simulation time: 1200 ps
dt = 0.004 ;time step in picoseconds
nsteps = 300000 ;number of steps
nstxout = 1000 ;frequency to write coordinates to output trajectory file
nstvout = 1000 ;frequency to write velocities to output trajectory file
nstlog = 1000 ;frequency to write energies to log file
nstenergy = 100 ;frequency to write energies to energy file
nstxtcout = 1000 ;frequency to write coordinates to xtc trajectory
xtc_grps = ;group(s) to write to xtc trajectory
energygrps = ;group(s) to write to energy file
nstlist = 5 ;Frequency to update the neighbor list (and the long-range forces,when using twin-range cut-off's).
ns_type = grid ;Make a grid in the box and only check atoms in neighboring grid cells
rlist = 0.9 ;cut-off distance for the short-range neighbor list
coulombtype = PME
rcoulomb = 0.9
vdwtype = switch
rvdw_switch = 0.5
rvdw = 0.8 ; long range Van der Waals cut-off
;rvdw = 0.9 ;treatment of van der waals interactions
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
pbc = xyz ; Periodic boudary conditions in all the directions
;Temperature coupling
tcoupl = berendsen
tc-grps = SOL DNA
tau_t = 0.1 0.1
ref_t = 300 300
;Simulated Annealing
;annealing = single single
;annealing_npoints = 3 3
;annealing_time = 0 1 4 0 1 4
;annealing_temp = 300 300 300 300 300 300
;Velocity generation
gen_vel = yes
gen_temp = 300
gen_seed = 173529
;Constrain all bonds
constraints = all-bonds
-------------- next part --------------
# This file was created Fri May 19 15:22:52 2006
# by the following command:
# g_rms_d -s DNA8_mdEq.tpr -f mdEq_traj.trr -n indexAcqua.ndx -o rmsd2D_3.xvg
#
# g_rms_d is part of G R O M A C S:
#
# Good ROcking Metal Altar for Chronical Sinners
#
@ title "RMSD"
@ xaxis label "Time (ps)"
@ yaxis label "RMSD (nm)"
@TYPE xy
@ subtitle "System after lsq fit to System"
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