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

[vivek sinha]

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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