[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
viveksinha20002 at gmail.com
Mon Jul 14 02:14:25 CEST 2014
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 <
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to
; 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
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.
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
> 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
>> 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 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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