NPT then NVT simulation in a single config file for water box?

From: Tanooj Shah (
Date: Fri Oct 30 2020 - 21:52:19 CDT


I wanted to ask if it is possible to run an NPT simulation for a certain
number of frames and then subsequently an NVT simulation starting from
the coordinates at the end of the NPT part. I believe it is possible to
do this in separate config files but I am getting some inconsistent
results which is why I wanted to ask if it possible to modify the config
file to perform both (similar to how in LAMMPS you would write a fix,
unfix and then another fix command).

Specifically, I am trying to run a simulation of just a water box. It
didn't seem clear how to create a box of water purely from scratch so I
did it in a roundabout way - I wrote a pgn script to create a sodium
ion, added a solvation box around it, and then wrote another pgn script
to delete the sodium ion. Not sure if there is a cleaner way to fill a
simulation box with water and nothing else.

I initially ran an NPT simulation at T=300K,
LangevinPistonTarget=1.01325 bar (the default) and averaged the density
of the water in the box over all frames and got a result of around 0.94
g/cm3, which is lower than the expected water density for the TIP3P
model (0.98 g/cm3). I increased the LangevinPistonTarget until I was
able to get a stable density of 0.98 g/cm3 (this was at a
LangevinPistonTarget of around 875 atm, I had to try multiple different
values to get the "correct" density).

I used the last frame of the .coor file as an input pdb file (and
generated a corresponding psf file) to an input to an NVT simulation
with a slightly reduced cell size (to match the compression from the NPT
run). However at the end of the NVT run I am still getting a density too
low - around 0.92 g/cm3. However I suspect this might be because the new
cell size is not exact.

I have two questions mainly - one, is is it possible to run an NPT and
an NVT simulation in the same config file? And the second is more
general and not sure if it is appropriate to post here - why am I
getting a simulation lower than 0.98 g/cm3 for water at STP? Is this
happening because when I deleted the sodium ion that created a void? Is
there a way to create a solvation box for "no" atoms so the entire
simulation box is uniformly filled with water?

Thank you if you took the time to read this entire message.


Tanooj Shah
Materials Science Department
Rensselaer Polytechnic Institute

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