Hey :)
Since pressure is so ill-defined at those volumes, you may as well run NVT
then at a more or less plausible volume. That will relieve the worry that
the deviations from the intended physics (in light of the force field
chosen) will cause the system to expand or contract out of control and y
maybe just a historical curiosity, but small systems with only 100
molecules or so and cutoffs of 0.7 nm were considered as best practices,
maybe even state-of-art, in computer simulations of liquids:
J. Chem. Phys. 79, 926 (1983); http://dx.doi.org/10.1063/1.445869
nowadays you have to use syste
you are on the right way.
set high pressure.
set cut-offs to half box side.
run classical MD, ~10 000 steps, and, afterwards, manually increase the box
sides to mimic the experimental density
in the plane-wave DFT, run local optimization prior to AIMD.
On Tue, Feb 16, 2016 at 4:01 PM, M
Mark
Abraham
[mark.j.abra...@gmail.com] Sent: 16 February 2016 20:06 To:
gmx-us...@gromacs.org Subject: Re: [gmx-users] NPT equilibration with
small
cell
Hi,
The cut-offs are not free parameters. The quality of the model physics
depends on them (details are complex). Thus there is a minimum
[gmx-users] NPT equilibration with small
cell
Hi,
The cut-offs are not free parameters. The quality of the model physics
depends on them (details are complex). Thus there is a minimum cell size that
is workable with typical force fields.
Mark
On Tue, 16 Feb 2016 19:02 Miguel Caro wrote:
Hell
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham
[mark.j.abra...@gmail.com]
Sent: 16 February 2016 20:06
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] NPT equilibration with small cell
Hi,
The
Hi,
The cut-offs are not free parameters. The quality of the model physics
depends on them (details are complex). Thus there is a minimum cell size
that is workable with typical force fields.
Mark
On Tue, 16 Feb 2016 19:02 Miguel Caro wrote:
> Hello,
>
> I was wondering if there is any reason
Hello,
I was wondering if there is any reason why one should expect a constant
pressure simulation not to work for a small cell. I am running a very
small cell (1.2 nm^3) simulation because I need it as input for ab
initio MD. I am trying to simulate NPT at 1 atm and it seems like my
cell, a
