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

[BON Michael]

Hi and thanks,

The pressure is stable, the mean value is -280 bar, which sounds normal, and it is isotropic (Pres-XX = Pres-YY = Pres-ZZ = -280 bar)

I also tried with no constraint (I forgot to mention it in my previous mail) but it didn't solve anything.

I did a proper energy minimization, there is no warning, error message, wierd energy at any moment. Moreover, I tried to simulate many different systems, doing each time a good minimization, and I always get this strange behaviour.

Michael Bon



Message: 6
Date: Tue, 14 Aug 2007 23:09:53 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Long-term drift, crash
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <46C1A9A1.3060207 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

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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