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

[Mark Abraham]

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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