[gmx-users] System Exploding
Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 26 14:02:44 CET 2012
Alex Seling wrote:
> Given the unfavorable input, then, it seems odd then that the same .mdp
> and protein ran consistently on 4.0.7, and I can't seem to find anything
> in the changelog to indicate a relevant change.
There are numerous algorithmic changes in the 4.5.x series. Many people have
reported the same problem you have (something works in 4.0.x and not 4.5.x) and
the solution is to set nsttcouple (and, if applicable, nstpcouple) to 1 for an
initial equilibration phase. The default is to have nsttcouple = nstlist,
which, in your case, is very infrequent.
Then, once the system is relaxed, you can remove this (very) frequent updating.
The coupling algorithms in 4.0.x were more relaxed, such that a system that
was not necessarily well-optimized might have had better odds of "working" (i.e.
surviving), but as I understand it, the new algorithms are, overall, more robust.
> On Thu, Jan 26, 2012 at 1:26 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> On 26/01/2012 5:10 PM, Alex Seling wrote:
>> After upgrading to gromacs 4.5.5, the old .mdp file that was
>> working is now giving me errors.
> Marginally stable numerical integration can work out, or not. Here,
> you are using a time step that is not suitable for a simulation
> lacking bond constraints. See section 6.5 of manual, for example. If
> you really want infinite cut-offs, read 7.3.9. Normal practice to
> avoid problems is to use an equilibration regime whose integration
> scheme is more gentle than your simulation regime.
>> Specifically, I'm getting
>> "This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size"
>> for a few interactions, with each of them approaching inf.
>> This is with a good starting configuration. Any ideas as to the
>> error? My .mdp file is below.
>> Alex Seling
>> title = lea at 300K
>> cpp = /lib/cpp -traditional
>> integrator = md ;sd ;md ;bd
>> tinit = 0.0
>> dt = 0.001 ;time step of 1 fs
>> nsteps = 238000000 ;1 us @ 1fs
>> nstxout = 200000 ; frequency to write coordinates to output
>> trajectory file = 1ns
>> nstxtcout = 200000 ; frequency to write coordinates to xtc
>> trajectory = 1 ns
>> nstvout = 0
>> nstfout = 0
>> nstlog = 200000 ; frequency to write energies to log file = 1 ns
>> nstenergy = 200000 ; frequency to write energies to energy file = 1ns
>> energygrps = system
>> comm_mode = angular
>> nstcomm = 40
>> nstlist = 100
>> nstype = simple
>> pbc = no
>> rlist = 100
>> rgbradii = 100
>> coulombtype = cut-off
>> epsilon_r = 1 ; double check this is what we want
>> rcoulomb = 100
>> vdwtype = cut-off
>> rvdw = 100
>> tc-grps = system
>> tau_t = 0.01099
>> ref_t = 300
>> gen_vel = yes
>> gen_temp = 273
>> constraints = none
>> implicit_solvent = GBSA
>> gb_algorithm = OBC
>> gb_epsilon_solvent = 78
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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