[gmx-users] Check for bad contacts and/or reduce the timestep.

[Justin A. Lemkul]

shivangi nangia wrote:
> Hello gmx-users,
> 
> I have a 5 ang box with equal number of water and methanol molecules 
> (1800), a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system 
> is overall +2 charged.
> 

If your box truly is 5 A (0.5 nm), grompp should have failed based on your 
cutoffs.  I assume you have a 5-nm box?

> I am trying to to do a NVT equilibration which runs into the following 
> error:
> 
> 
> t = 0.000 ps: Water molecule starting at atom 11816 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> 

Did you do energy minimization first?  If so, what was the outcome?  Were the 
energies and forces acceptable?  What force field are you using?  The generic 
information about your problem can be found at:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

> the nvt.mdp is:
> 
> title    = hist NVT equilibration
> define      = -DPOSRES  ; position restrain the protein
> ; Run parameters
> integrator  = md     ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt    = 0.002    ; 2 fs
> ; Output control
> nstxout     = 100    ; save coordinates every 0.2 ps
> nstvout     = 100    ; save velocities every 0.2 ps
> nstenergy   = 100    ; save energies every 0.2 ps
> nstlog      = 100    ; update log file every 0.2 ps
> ; Bond parameters
> continuation   = no     ; first dynamics run
> constraint_algorithm = lincs  ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
> lincs_iter  = 1      ; accuracy of LINCS
> lincs_order = 4      ; also related to accuracy
> ; Neighborsearching
> ns_type     = grid      ; search neighboring grid cells
> nstlist     = 5      ; 10 fs
> rlist    = 1.0    ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.0    ; short-range electrostatic cutoff (in nm)
> rvdw     = 1.0    ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME    ; Particle Mesh Ewald for long-range electrostatics
> pme_order   = 4      ; cubic interpolation
> fourierspacing = 0.16      ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl      = V-rescale ; modified Berendsen thermostat
> tc-grps     = Protein Non-Protein   ; two coupling groups - more accurate
> tau_t    = 0.1 0.1   ; time constant, in ps
> ref_t    = 250    250   ; reference temperature, one for each group, in K
> ; Pressure coupling is off
> pcoupl      = no     ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc      = xyz    ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = yes    ; assign velocities from Maxwell distribution
> gen_temp = 250    ; temperature for Maxwell distribution
> gen_seed = -1     ; generate a random seed
> 
> I did try to reduce the timestep from 2 fs to 1 fs but ran into the same 
> error.
> 
> 
> 
> Searching through a few archives I got a hint it is something do to with 
> water's density per cubic nm.
> Is that whats going on here?
> If yes, then how do I randomly delete some water molecules from my system?
> 
> Please help.
> 
> Thanks,
> Shivangi
> 
> 
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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