[gmx-users] A question about "blowing up"

[sujithkakkat .]

Hello,

   I am following justin lemkul's tutorials for the cyclohexane-water
biphasic system using Gromos96 forcefield.
Things went well till NVT equilibration where I had this "Blowing up" issue.

 Shortening the time step alone did not help, and it was difficult for me
to figure out what was happening from watching the trajectory.
 g_energy  data indicated a spike on the,  short range LJ contribution at
around 10ps.

  Then I switched off the constraints (but not for water, SETTLE still
used) and ran the simulation again with a small time step. Things worked
well this time , the system reaching the target temperature.

 I want to make sure that switching off the constraints is a reasonable
thing to solve Blowing up and that it would not affect in any way the
accuracy of further simulations.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up  says that
constraints are exactly not the source of the Blowing up problem.
However,
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
suggests removing constraints as a solution.

     So, in general, is the problem solved by removing constrains, or am I
cheating? Please comment.

Here is the .mdp file which solved the Blowing up issue.

; 7.3.3 Run Control
integrator              = md
tinit                      = 0
dt                         = 0.0002
nsteps                  = 2500000
comm_mode         = Linear
nstcomm              = 1
comm_grps           = CHX SOL

; 7.3.8 Output Control
nstxout                 = 25000
nstvout                 = 25000
nstfout                  = 25000
nstlog                   = 100
nstenergy              = 100
nstxtcout               = 100
xtc_precision          = 1000
xtc_grps                 = System
energygrps              = System

; 7.3.9 Neighbor Searching
nstlist                    = 1
ns_type                 = grid
pbc                       = xyz
rlist                       = 0.9

; 7.3.10 Electrostatics
coulombtype             = PME
rcoulomb                   = 0.9

; 7.3.11 VdW
vdwtype                 = cut-off
rvdw                      = 1.4
DispCorr                 = EnerPres

; 7.3.13 Ewald
fourierspacing          = 0.12
pme_order               = 4
ewald_rtol                = 1e-5

; 7.3.14 Temperature Coupling
tcoupl                   = berendsen
tc_grps                 = CHX        SOL
tau_t                     = 0.1        0.1
ref_t                     = 298        298

; 7.3.17 Velocity Generation
gen_vel                   = yes
gen_temp                = 298
gen_seed                 = -1

; 7.3.18 Bonds
constraints                 = none
constraint_algorithm    = LINCS
continuation                = no
lincs_order                  = 4
lincs_iter                     = 1
lincs_warnangle           = 30
~


Thanks,

Sujith.