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. 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): 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 Please ask for any additional information if you have an idea of where this problem comes from. Many thanks, Michaël Bon
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