[gmx-users] system explodes
Justin A. Lemkul
jalemkul at vt.edu
Tue Nov 11 22:47:12 CET 2008
Andrea Muntean wrote:
> I am simulating one chain of PS. The box is produced by pdb2gmx. If I
> run simulations with timestep 0.1 fs up to 0.4 fs everything seem to
> be ok. With 1 fs (which should be a normal time for my system) I would
> get the following warning:
> Warning: 1-4 interaction between 290 and 299 at distance 108.224 which
> is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> The parameters I use are the following:
> title = PS
> cpp = /lib/cpp
> integrator = md
> dt = 0.0001 ; ps !
> nsteps = 10000 ; total 10 ps
> nstlist = 10
> nstxout = 100
> nstvout = 100
> nstenergy = 100
> unconstrained-start = yes
> nstxtcout = 50
> nstlog = 50
> constraints = none
> ns_type = grid
> vdwtype = Cut-off
> fourierspacing = 0.055 ; Lbox/0.055 ~ 50
> rlist = 0.9
> rvdw = 1.2
> tc_grps = system
> tcoupl = berendsen
> tau_t = 0.1
> ref_t = 540
> Pcoupl = no
> optimize_fft = yes
> the rest is set default
> Did I miss something? What goes wrong?
You are running a very high temperature with no bond constraints. I would
expect you would need a very small timestep (like 0.1 fs) to get reasonable
dynamics. Try using constraints.
> Any help and/or comments are really appreciated.
> Thank you!
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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