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

Mark Abraham mark.j.abraham at gmail.com
Fri Sep 1 08:51:33 CEST 2017


These "gaps" are probably just what you expect with
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 ;-)


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,
> Ph.D Student
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