From: Tanooj Shah (shaht2_at_rpi.edu)
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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