[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
viveksinha20002 at gmail.com
Mon Jul 14 17:35:53 CEST 2014
I dont have the periodic molecules so do I include anything in the .mdp
file? Also when I grompp this I get no warning or error or note. But when I
mdrun it, I get
WARNING: Listed nonbonded interaction between particles 35 and 114
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.
and then the program terminates after displaying a segmentation fault error.
Please provide any valuable suggestions.
On Mon, Jul 14, 2014 at 8:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
>> 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 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
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