[gmx-users] Regarding NPT simulation and box length variation

[Mark Abraham]

Hi,

Note that I said solute, not solvent.

There are no relevant gaps after an effective NPT equilibration. The usual
force fields do not permit it.

"Gap" is a quite non-specific description, but the appearance of such is
usually because the contents of the simulation cell look like a jigsaw
piece (that obviously tessellates with itself). If you still think you have
an issue, please upload some images to a file-sharing service and share us
a link.

Mark

On Fri, Sep 1, 2017 at 10:12 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Sir,
> There is no any solvent that is protruding outside the box...all the
> molecules are within the box itself, and still i am able to view the
> gaps/empty area at some regions in the box...(which is indicating that the
> box length is slightly bigger)
> So how can i make sure that there are no any gaps in my box system and
> hence proceed or further compress the box ..
>
> These gaps can affect the analysis part like during calculating rdf, cn,
> hydrogen bond dynamics, etc...i hope so... Or doen't it affect... any
> ideas..??
>
> Thank you...
>
>
>
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> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
>
> On Fri, Sep 1, 2017 at 12:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > These "gaps" are probably just what you expect with
> > http://www.gromacs.org/Documentation/Terminology/
> > Periodic_Boundary_Conditions
> > for
> > the configuration you are viewing. For example, if the solute protrudes
> out
> > one side of the box, then there will be a matching gap on the other side
> of
> > the box, because that's what PBC means. If you want to view a
> space-filled
> > box, then you need to e.g. use trjconv to make it so.
> >
> > NPT isn't going to tolerate a region of vacuum ;-)
> >
> > Mark
> >
> > On Fri, Sep 1, 2017 at 8:32 AM Dilip H N <cy16f01.dilip at nitk.edu.in>
> > wrote:
> >
> > > Hello,
> > > I am having a peptide and  water mixture in a cubic box of say 2.5 2.5
> > 2.5
> > > nm. and if i view in vmd i am able to see there are empty spaces/gaps
> at
> > > some areas/regions (or in other words the box length is slightly
> bigger),
> > > so i ran the energy minimization(with em.mdp) and followed by npt
> > > simulation (with npt.mdp), to know the box length by allowing it to
> > > fluctuate...
> > > But after npt simulation if i view the final structure/full trajectory
> in
> > > vmd, the box length has decreased slightly, but still i am able to see
> > > there are empty spaces/gaps within the box. Is it ok with the gaps at
> > some
> > > areas or the molecules should be compactly arranged within the box..??
> > >
> > > I am trying with the following commands:-
> > > gmx insert-molecules -f abc.gro -ci def.gro -nmol xxx -o ghi.gro     #
> > > inserting molecules
> > > gmx solvate -cp ghi.gro -cs spc216.gro -o jkl.gro -maxsol xxx        #
> > > solvating with water
> > > gmx grompp -f em.mdp -c jkl.gro -p topol.top -o em.tpr
>   #
> > > energy minimization
> > > gmx mdrun -v -s em.tpr -deffnm em
> > > gmx grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr
> #
> > > npt simulation
> > > gmx mdrun -v -s npt.tpr -deffnm npt
> > >
> > > The gmx solvate command solvates with the empty spaces... and still
> after
> > > energy minimization and npt simulation i am able to see some gaps in
> the
> > > box through vmd.
> > > How to get rid of these spaces inside the box.. or get the box
> compressed
> > > still further with whole mixture of molecules are within the box.
> > > So how can i solve this issue..?? Do i need to modify anything in the
> > .mdp
> > > files..or any where else..??
> > > Here are the em.mdp and npt.mdp files attached...
> > >
> > > Any suggestions are highly appreciated ....
> > >
> > > Thank you...
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > >
> > >
> > >
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> > > >
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> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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