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

[shivangi nangia]

Hello,

I am sorry, I did mean 5 nm box.

I did do the energy minimization but somehow overlooked the error message at
that stage.

Things seems to be working now.

Thanks for the time.

Shivangi

On Tue, Mar 29, 2011 at 2:06 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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