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

Dallas Warren Dallas.Warren at monash.edu
Wed Jul 16 07:29:03 CEST 2014 

You are just removing waters, so unless it is mixed up with the tube (which it shouldn't be), then the topology doesn't care.  All it really cares about is the atom names and the order.  Your topology should be something like (the .itp could be included within the .top):

CNT.itp will contain
[ moleculetype ]
CNT
[ atoms ]
....
[ bonds ]
...
Etc

topol.top will contain
#include "CNT.itp"
#include "correct water model.itp"
[ system ]
CNT with water outside only
[molecules ]
CNT    1
SOL    some large number

conf.gro will contain
CNT with water outside only
 somelargenumber
    1CNT  C1     1   x y z
....
some#SOL  OW some#   x y z
some#SOL HW1 etc

As long as the order in the topology and the coordinate file matches all will work.

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 3:15 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem related to solvating CNT and then
> removing out the molecules inside CNT
> 
> 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
> > > >>
> > > >> ==================================================
> > > >> --
> > > >> Gromacs Users mailing list
> > > >>
> > > >> * Please search the archive at http://www.gromacs.org/
> > > >> Support/Mailing_Lists/GMX-Users_List before posting!
> > > >>
> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >>
> > > >> * For (un)subscribe requests visit
> > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-
> users
> > > or
> > > >> send a mail to gmx-users-request at gromacs.org.
> > > >>
> > > >
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
> 
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list