[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
viveksinha20002 at gmail.com
Wed Jul 16 06:53:11 CEST 2014
I will tell you the steps that I took for the simulation from the beginning.
1. Generated a tube online
2. Attched Hydrogen to it using pymol and converted to .gro and then .top
3. Solvated using genbox -cp cnt_sl.gro -cs spc216.gro -o cnt_solvated.gro
4. Remove atoms from center using c++ script which does not numbers the
atoms again. My 12663 atoms changed to 12183 after this.
5. Energy minimisation: grompp -f minim.mdp -c ___.gro -p ___.top -o em.tpr
mdrun -v -deffnm em
The next step about equibilating is giving a segmentation fault.
The minim.mdp 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 = 0.9 ; Short-range electrostatic cut-off
rvdw = 0.9 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
And I have already sent you the nvt.mdp settings that I am using.
Please help me in completing my simulation.
On Wed, Jul 16, 2014 at 1:25 PM, vivek sinha <viveksinha20002 at gmail.com>
> But mdrun doesnt update these information/new numbering in the topology
> file. I mean the topology fie would be saying that there is a bond between
> 101 and 105 and if I removed those atoms, the mdrun would have assignmed
> 101 and 105 to some other atom and hence it can create problems.
> Is this possible?
> On Wed, Jul 16, 2014 at 9:35 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 7/15/14, 2:19 PM, vivek sinha wrote:
>>> Hey Justin,
>>> I think I understood the problem. When I removed the solvent from inside
>>> CNT, I kept the numbering of atoms just like before without actually
>>> a new strictly increasing order numbering. But now when I see that after
>>> the energy minimization the new pdb file got arranged strictly by
>>> increasing order.
>>> As an example. After deleting atoms inside the CNT, my .gro file did not
>>> had the atom no 6292, but after energy minimisation the em.gro file
>>> contains the atom no 6292. This must have created a renumbering of the
>>> atoms. Not good I suppose.
>>> Please suggest what to do?
>>> The concern is that whether to renumber the molecules after removing the
>>> water from inside the CNT or not?
>> The numbering in the input coordinate file is irrelevant. The output of
>> mdrun is always numbered consecutively from 1.
>> 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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