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

[vivek sinha]

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.

Thanking you,
Vivek Sinha


On Mon, Jul 14, 2014 at 1:39 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/13/14, 12:31 PM, vivek sinha wrote:
>
>> What changes in topology file should I do? Just the number of water
>> molecules?
>>
>
> Yes.  If you removed waters, that must be reflected in the number of
> molecules listed in the topology.
>
>
>  But I have also changed the atom number of each molecule while removing
>> the
>> molecules from inside.
>>
>> In other words my new .gro file also has the atom numbers in increasing
>> order with no gap.
>>
>>
> grompp doesn't care about the numbering in the .gro file.
>
>
> -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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