[gmx-users] system explodes

[Andrea Muntean]

Thank you. I will do so.

kind regards,
Andrea

2008/11/11 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> 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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>
> --
> ========================================
>
> 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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