[gmx-users] System Exploding
selingal at msu.edu
Thu Jan 26 13:00:00 CET 2012
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.
On Thu, Jan 26, 2012 at 1:26 AM, Mark Abraham <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
> 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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