Yup. Didn't even notice.
On Mon, Aug 6, 2018, 12:50 PM Justin Lemkul wrote:
>
>
> On 8/6/18 9:07 AM, Lucia Mydlova wrote:
> > Thank you very much for your helpful advice.
> >
> > I simulated polymer PMMA with two organic chromophores in NVT ensemble
> for
> > 2ns and, the same system one more
On 8/6/18 9:07 AM, Lucia Mydlova wrote:
Thank you very much for your helpful advice.
I simulated polymer PMMA with two organic chromophores in NVT ensemble for
2ns and, the same system one more time for 1.5ns
with parameters:
constraints = none
integrator = md
dt
The generally accepted protocol for simulations that end up running in
NPT is EM > relaxation NPT (possibly a series of relaxations) >
production NPT. You will almost certainly see high pressure fluctuations
right after NVT, especially given your extremely short timescales. Also,
your tau_t is
Thank you very much for your helpful advice.
I simulated polymer PMMA with two organic chromophores in NVT ensemble for
2ns and, the same system one more time for 1.5ns
with parameters:
constraints = none
integrator = md
dt = 0.001
nsteps =
On 8/3/18 3:57 AM, Quyen V. Vu wrote:
Hi,
please check this:
http://www.gromacs.org/Documentation/Terminology/Pressure
Usually, if your system contains more than one element, use one thermostat
and barostat for solvent, one for the solution will give you more precise
instead of group system
Hi,
please check this:
http://www.gromacs.org/Documentation/Terminology/Pressure
Usually, if your system contains more than one element, use one thermostat
and barostat for solvent, one for the solution will give you more precise
instead of group system for all
On Fri, Aug 3, 2018 at 2:14 PM
I think calling this community "customers" is very funny. ;)
Pressure fluctuations depend on the system composition, size its
starting state (how well and for how long it was equilibrated), and many
other things. Further, pressure is not supposed to be dead-on constant
and some degree of
Hello,
what do you mean with the pressure not being constant? If you mean the
fluctuations in the instantaneous pressure, this is normal. What should
be constant is the time average of the pressure over the time of the
simulation.
I don't see anything particular in your mdp file that could
Dear all customers.
I have a problem, in my NPT simulations the pressure is not constant and
the temperature is. Earlier simulation in NVT conditions was ok. I use
these parameters:
tcoupl = nose-hoover
tc_grps = system
tau_t = 0.002
ref_t
