From: Hemanth Haridas (hemanth.h_at_iitgn.ac.in)
Date: Tue Nov 03 2020 - 00:27:18 CST
1. Specifically, I am trying to simulate 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.
*You can generate a pure solution box by using CHARMM-GUI server, which
will create a water box of required dimensions.*
2. 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.
*You can run that using restart files generated at the end of the NPT
equilibration run. You must set the first timestep to the last timestep of
your NPT run when you start your NVT run. You will need two config files,
one for NPT and other for NVT.*
On Sun, Nov 1, 2020 at 9:12 PM Tanooj Shah <shaht2_at_rpi.edu> wrote:
> Just as a follow up to this question in case anyone read it - I did
> triage the modified simulation box size after the first NPT run and
> after using that in the NVT simulation did get a consistent reading for
> the density of TIP3P water (0.98 g/cm3). I am guessing this was because
> the void left after deleting the sodium ion needed to be filled. I
> suspect there must be a way to write a pgn script to replace the sodium
> ion with a water molecule without all three water atoms overlapping.
> However I would still like to ask if it possible to add a solvation box
> with "no" molecules (i.e. an empty pdb and psf input file).
> On 2020-10-30 22:52, Tanooj Shah wrote:
> > Hello,
> > 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.
> > Best,
> Tanooj Shah
> Materials Science Department
> Rensselaer Polytechnic Institute
-- *Hemanth H 18310019* Research Scholar IIT Gandhinagar
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