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

[vivek sinha]

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
oplsaa.

Thanks in Advance,
Vivek Sinha


On Mon, Jul 14, 2014 at 10:39 AM, vivek sinha <viveksinha20002 at gmail.com>
wrote:

> 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
>>> minimization)
>>> 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
>>> to
>>> perform
>>>
>>> ; Parameters describing how to find the neighbors of each atom and how to
>>> calculate the interactions
>>> nstlist            = 1            ; Frequency to update the neighbor list
>>> and long range forces
>>> cutoff-scheme   = Verlet
>>> ns_type            = grid        ; Method to determine neighbor list
>>> (simple, grid)
>>> coulombtype        = PME        ; Treatment of long range electrostatic
>>> interactions
>>> 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
>>
>> --
>> ==================================================
>>
>> 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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>
>