[gmx-users] system explodes
andreamuntean at gmail.com
Tue Nov 11 23:09:46 CET 2008
Thank you. I will do so.
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.
>> Any help and/or comments are really appreciated.
>> Thank you!
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> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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