[gmx-users] RE : long-term drift and crash

BON Michael michael.bon at cea.fr
Tue Aug 21 12:55:00 CEST 2007


Sorry fot no answering accurately.
Here is new insight for understanding my problem.

In fact, even simulations of pure water (tip4p and tip4p_ew) don't work !
And those simulations crash with a strange periodic pattern : still using g_msd, I observe
on the msd plot sudden jumps that occur exactly every 10.000 ps ! By "jump" I mean a violent
increase of the slope of the curve that lasts a short time, which is exactly 0.1 ps each time in my case. The curve is linear with the correct diffusion constant otherwise. I observe such jumps between 10.0 and 10.1 ps, 20 and 20.1 ps 30 and 30.1 ps, and so on, and each time the jumps have a higher magnitude than the previous one, till the simulation crashes.

I don't see anything in my parameters that could explain such a periodicity of 10.000 ps. I tried to half the timestep, and it halved the duration of the jump, which thus became 0.05, but it didn't changed the periodicity of 10 ps. Changing tau_t had no consequence.

Here are again my parameters for water simulation : 
constraints = all-bonds
constraint_algorithm = Lincs
lincs_order = 4
integrator = md
dt = 0.002
nsteps = 1000000
comm_mode = none
coulomb_type = PME
fourier_spacing = 0.12
optimize_fft = yes
vdwtype = cut-off
rcoulomb = 1.2
rvdw = 1.2
rlist = 1.2
DispCorr= EnerPres
nstlist = 1
ns_type = grid
pbs = xyz
tcoupl = berendsen
tc-grps = System
tau_t = 0.5
ref_t = 300
pcoupl = no
gen_vel = yes
gen_temp = 300

I am still using AMBER99, and the include files ffamber_tip4p.itp and ffamber_tip4p_ew.itp, in double precision. With g_energy,  everything looks normal, I even find an average potential energy of 41.23 kJ/mol per tip4p water molecule, which is a published value. What is going on ?!

Thanks for your time and help,
Michael Bon

Message: 2
Date: Sat, 18 Aug 2007 12:34:02 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Re : long-term drift and crash
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <46C65A9A.5090103 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

BON Michael wrote:
> The same bugs occurs during the NPT equilibration stage that I did after the energy minimization (with l-bgfs, till convergence), the average pressure being now -0.5 bar (over the 200 ps the simulation ran before it crashed).
> Still the same things : everything I plot with g_energy is normal, the msd plot oscillates more and more, I see nothing special on the last configuration just before the crash).

Actually that link suggests some NVT to fix temperatures and NPT to fix 
box size. It sounds like your system is fragile and you should be doing 
both of these... or at least telling us that you're doing both of these.


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