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

[Dilip H N]

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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