[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT

[Justin Lemkul]

On 7/14/14, 12:28 AM, vivek sinha wrote:
> Hey Justin,
> I am really having a hard time using GROMACS for my simulation. When trying
> to equilibrate in NVT ensemble I am getting this warning.
> ---------------
> WARNING: Listed nonbonded interaction between particles 227 and 230
> at distance 3f which is larger than the table limit 3f nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
> ------------------
>   Can you please look over my nvt.mdp file
>
> ------------------
> title        = CNT in water
> 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        = 500        ; save coordinates every 1.0 ps
> nstvout        = 500        ; save velocities every 1.0 ps
> nstenergy    = 500        ; save energies every 1.0 ps
> nstlog        = 500        ; update log file every 1.0 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
> cutoff-scheme   = Verlet
> ns_type            = grid        ; search neighboring grid cells
> nstlist            = 10        ; 20 fs, largely irrelevant with Verlet
> rcoulomb        = 0.9        ; short-range electrostatic cutoff (in nm)
> rvdw            = 0.9        ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype        = PME    ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order        = 4        ; cubic interpolation
> fourierspacing    = 0.12    ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl        = V-rescale                ; modified Berendsen thermostat
> tc-grps        = non-water SOL    ; two coupling groups - more accurate
> tau_t        = 0.1      0.1           ; time constant, in ps
> ref_t        = 300       300           ; 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    = 300        ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
> --------------------------
>
> Please suggest how can I correct the problem.
>

If the CNT is infinite along some axis, you need to use the periodic_molecules 
keyword, otherwise bonded interactions are assigned totally within the unit cell 
and you get nonsensical geometry.

As to your other question, cutoffs of 1.0 are commonly used with OPLS.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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