[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
viveksinha20002 at gmail.com
Mon Jul 14 06:28:19 CEST 2014
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
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
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)
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.
Thanking You in Advance,
On Mon, Jul 14, 2014 at 12:06 PM, vivek sinha <viveksinha20002 at gmail.com>
> Hey Justin,
> Can you tell me what should be the cutoff for the force field oplsaa. I am
> having the problem of "Listed nonbonded interaction between particles 51
> and 812 at distance 3f which is larger than the table limit 3f nm." and I
> have gone through the user gmx errors mail. You have answered one of
> similar doubts but haven't given the cutoff values for the forcefield
> Thanks in Advance,
> Vivek Sinha
> On Mon, Jul 14, 2014 at 10:39 AM, vivek sinha <viveksinha20002 at gmail.com>
>> Thanks Justin. That was very helpful. I have completed the energy
>> minimization successfully.
>> On Mon, Jul 14, 2014 at 9:16 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> On 7/13/14, 8:14 PM, vivek sinha wrote:
>>>> Thanks Justin.
>>>> But when I am trying to run the energy minimization I get the
>>>> error message "No such moleculetype SOL"
>>>> The minim.mdp file that I am using for energy minimization is:
>>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>>> integrator = steep ; Algorithm (steep = steepest descent
>>>> emtol = 1000.0 ; Stop minimization when the maximum force <
>>>> 1000.0 kJ/mol/nm
>>>> emstep = 0.01 ; Energy step size
>>>> nsteps = 50000 ; Maximum number of (minimization) steps
>>>> ; Parameters describing how to find the neighbors of each atom and how
>>>> calculate the interactions
>>>> nstlist = 1 ; Frequency to update the neighbor
>>>> and long range forces
>>>> cutoff-scheme = Verlet
>>>> ns_type = grid ; Method to determine neighbor list
>>>> (simple, grid)
>>>> coulombtype = PME ; Treatment of long range electrostatic
>>>> rcoulomb = 1.0 ; Short-range electrostatic cut-off
>>>> rvdw = 1.0 ; Short-range Van der Waals cut-off
>>>> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>>>> Can you please suggest how to solve this error.
>>> The only modification to your topology that you need to make is to
>>> adjust the number of SOL molecules in the [molecules] directive. Doing
>>> that won't give rise to this error. The error itself is telling you that
>>> the SOL moleculetype has not been declared, i.e. you have not #included a
>>> water topology appropriately.
>>> 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
>>> Gromacs Users mailing list
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