[gmx-users] Check for bad contacts and/or reduce the timestep.
shivangi.nangia at gmail.com
Tue Mar 29 21:28:25 CEST 2011
I am sorry, I did mean 5 nm box.
I did do the energy minimization but somehow overlooked the error message at
Things seems to be working now.
Thanks for the time.
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
>> 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:
> 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
>> 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.
> 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
> gmx-users mailing list gmx-users at gromacs.org
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