BON Michael wrote:
Hi,
I have been struggling for some time with a nasty problem with my simulations
of RNA in water
using Gromacs 3.3.1 and the AMBER ports. Nobody ever reported it so I am afraid
I did some
obvious mistake that I just cannot see.
After some steps (between 50000 and 150000), my simulations crash, and I hardly
found a good
reason for it : the only clue I found is given by a MSD analysis of the RNA (with g_msd) : the diffusion,
theoretically linear over time, is disturbed by sinusoidal-like noise whose magnitude increase
over time. Instead of <x²> = 6Dt, I see something that looks like 6Dt +
a*t*sin(2*Pi*t/T), where
T is generally around 5 ps. After some time, the magnitude of this "noise"
becomes too big and
the simulation crashes.
All the energies look normal, even just before crash.
What about the pressure? Check all of the things that g_energy lets you
graph.
I tried to change a lot of things but I still face the same problem on Mac OS
X, Ithanium
cluster, simple precision, double precision, AMBER99, AMBER96, TIP3P, SPC,
TIP4P, TIP4PEW
Here is the standard .mdp file I am using (I have the impression I use the same
parameters as in
most published papers):
It doesn't look to be the problem, but you could try without constraints
constraints = all-bonds
constraint_algorithm = lincs
lincs_order = 4 ( or 6)
integrator = md
dt = 0.002
nsteps = 200000
comm_mode = Angular (or none)
nstcomm = 25
coulomb_type = PME (or cut-off)
fourierspacing = 0.12
optimize_fft = yes
vdwtype = cut-off (or switch)
rcoulomb = 1.2 (or anything else)
rvdw = 1.2 (or anything else)
rlist = 1.2 (or anything else)
nstlist = 1
nstype = grid
pbc = xyz
tcoupl = berendsen
tcgrps = RNA Other
tau_t = 0.5 0.5 (or lesser values)
ref_t = 300 300
pcoupl = no;
gen_vel = yes
gen_temp = 300
Have you done energy minimization before simulating?
Mark
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