[gmx-users] system explodes

[Justin A. Lemkul]

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.

-Justin

> Any help and/or comments are really appreciated.
> 
> Thank you!
> 
> Andrea
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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