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

Wed Jul 16 07:15:00 CEST 2014

But not renumbered in the topology file. That would be an issue then.

On Wed, Jul 16, 2014 at 2:01 PM, Dallas Warren <Dallas.Warren at monash.edu>
wrote:

> No idea if the numbering is an issue (doubt it), but if you want to get
> the atoms renumbered sequentially within a coordinate file, just pass it
> through editconf without any manipulations.  It will renumber things for
> you.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> > vivek sinha
> > Sent: Wednesday, 16 July 2014 2:53 PM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Problem related to solvating CNT and then
> > removing out the molecules inside CNT
> >
> > Hey Justin,
> > I will tell you the steps that I took for the simulation from the
> > beginning.
> > 1. Generated a tube online
> > http://turin.nss.udel.edu/research/tubegenonline.html
> > 2. Attched Hydrogen to it using pymol and converted to .gro and then
> > .top
> > file
> > 3. Solvated using genbox -cp cnt_sl.gro -cs spc216.gro -o
> > cnt_solvated.gro
> > -p topol.top
> > 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
> > 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        = 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.
> >
> > Thanking You,
> > Vivek Sinha
> >
> >
> >
> >
> >
> >
> > On Wed, Jul 16, 2014 at 1:25 PM, vivek sinha
> > <viveksinha20002 at gmail.com>
> > wrote:
> >
> > > 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
> > >>> making
> > >>> 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
> > >>
> > >> --
> > >> ==================================================
> > >>
> > >> 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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