I mean here seems to say conserved energy is tilde H [
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
]
On Sat, Oct 18, 2014 at 6:44 PM, Johnny Lu wrote:
> The conserved energy from g_energy, which I saw someone say is tilde H,
> drop more crazily if I use 1
The conserved energy from g_energy, which I saw someone say is tilde H,
drop more crazily if I use 1s coupling constant.
On Mon, Oct 13, 2014 at 5:52 PM, Mark Abraham
wrote:
> Hi,
>
> What is your target observable? What "got worse?"
>
> Mark
>
> On Mon, Oct 13, 2014 at 11:17 PM, Johnny Lu
> wr
Hi,
What is your target observable? What "got worse?"
Mark
On Mon, Oct 13, 2014 at 11:17 PM, Johnny Lu wrote:
> The simulation get worse in a new way.
>
> I see that thermostat scales velocity and may not fix numerical error in
> potential energy.
>
> On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu
The simulation get worse in a new way.
I see that thermostat scales velocity and may not fix numerical error in
potential energy.
On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu wrote:
> I just want something that will patch up the energy lost due to numerical
> error of NVE simulation of the system
I just want something that will patch up the energy lost due to numerical
error of NVE simulation of the system ran by mixed precision gromacs,
instead of a thermostat.
I hope the velocity rescaling is sufficiently uncorrelated with the motion
of the protein.
So far, the simulations ran 2.5 ns, a
> I guess, if I pick a coupling constant that is just small enough to keep the
energy conserved, I would get a NVT simulation that is as close as a NVE
simulation as possible.
> Is this correct?
Yes, but then at that point the thermostat isn't actually thermostatting.
The Bussi comment is merely
On page 014101-3, the Bussi paper (http://dx.doi.org/10.1063/1.2408420)
mentioned: "On the other hand, for coupling constant approaching
infinity,the Hamiltonian dynamics is recovered."
Does that means that for a large enough coupling constant, the velocities
are nearly not rescaled, and the dynami
I am not quite in the business of folding/unfolding protein.
On Sun, Oct 12, 2014 at 4:07 PM, Johnny Lu wrote:
> Thank you for pointing me to that paper. I took a quick look of it
> yesterday.
> Would the results in the paper stay the same, if the side chain rotations
> of a protein is investiga
Thank you for pointing me to that paper. I took a quick look of it
yesterday.
Would the results in the paper stay the same, if the side chain rotations
of a protein is investigated?
On Sun, Oct 12, 2014 at 3:30 PM, Michael Shirts wrote:
> > If we use thermostats, the thermostats will correct the
> If we use thermostats, the thermostats will correct the energy drop/raise
caused by numerical error (which acts as a fluctuating source/sink that may
not even follow the normal distribution), without causing additional
artifacts.
Thermostats correct SOME of the artifacts. It is not always clear
oh, i still mix up things. the numerical error might act as dissipation.
On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu wrote:
> Sorry that I misunderstood your post.
>
> Can compensating energy lost caused by numerical error with thermostat
> cause error in the probability distribution of thermodyn
Sorry that I misunderstood your post.
Can compensating energy lost caused by numerical error with thermostat
cause error in the probability distribution of thermodynamic variables and
distribution of conformations?
Below is just a guess. I don't understand the fluctuation dissipation
theorem enou
> The point was that if the energy leaves the system, then the system
is never in equilibrium. Not vice versa, please.
This is incorrect logic. f there are errors in the integrator, then
F=gradient of the potential is not true. If that is not true, energy is not
conserved, and energy can leave or
The point was that if the energy leaves the system, then the system is
never in equilibrium. Not vice versa, please.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu wrote:
> Why non-equilibrium can cause lost of total energy in NVE simulation?
> (bari
On 2014-10-12 17:31, Dr. Vitaly Chaban wrote:
The artifacts are caused by energy leakage. Thermostatting does not
solve them. The problem exists, but you do not see it clearly with
thermostat. For instance, I have an example where a liquid droplet in
vacuum is not stable due to bad energy conserv
Why non-equilibrium can cause lost of total energy in NVE simulation?
(baring the case that the non-equilibrium causes very large values that
causes over flow / getting out of the stable range of algorithms of
gromacs).
A closed system should have constant energy, regardless of whether it is at
eq
I believe the major problem with energy losses is that your system
never achieves equilibrium.
Thus, all the simulated properties are not what they need to be...
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sun, Oct 12, 2014 at 5:31 PM, Dr. Vitaly Chaban wrote:
> The artifacts are caus
The artifacts are caused by energy leakage. Thermostatting does not
solve them. The problem exists, but you do not see it clearly with
thermostat. For instance, I have an example where a liquid droplet in
vacuum is not stable due to bad energy conservation. Some particles
just sporadically fly away
Firstly, what are the possible errors/artifacts caused by masking "the
energy leakage problem with the thermostat" in this case?
Secondly, are there any other mdp setting that I can try to make the mixed
precision gromacs NVE run have conserved energy over 100 ns ? (and... is it
because of some e
Thus, what is your question now? :-)
The total energy must remain conserved at all times. That's it.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sun, Oct 12, 2014 at 2:45 AM, Johnny Lu wrote:
> I tried PME and then potential-shift-verlet for Van der Waals. The energy
> is still not
I tried PME and then potential-shift-verlet for Van der Waals. The energy
is still not constant in mixed precision gromacs 5.0.1 NVE run on 12 xeon
cpu without gpu. Those were nearly the last few things that I knew that I
can try in mixed precision. The system has ~165 amino acid, ~9000 water,
and
Well, if it does not conserve total energy, than such a computational
experiment is not reliable. This is a sad truth.
Philosophically, you have two options here. Either you accept that
energy leakage is significant and then you must fight against it
(smaller time-step, double precision, constrain
I tried NVE on single precision gromacs 4.6.7 with and without GPU.
The energy either drift down or up, depending on the mdp file, and the
drift seems linear.
Linear fit says that if I run 100 ns simulation, at the end the energy is
doubled.
If I use double precision gromacs, the drift seems insi
I also cannot get why not to just turn off the thermostat...
If energy transfer phenomena are in focus, NVE is an ensemble of
choice, no matter which relaxation constant is used for the T-coupling
algorithm.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sat, Oct 11, 2014 at 6:32 PM, Antoni
Then, run true NVE, for the reasons we already pointed.
On Sat, 11 Oct 2014, Johnny Lu wrote:
For dynamics with correct rate and correct fluctuation.
On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban
wrote:
what is it needed for?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Fri,
For dynamics with correct rate and correct fluctuation.
On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban
wrote:
> what is it needed for?
>
>
>
> Dr. Vitaly V. Chaban
>
> Виталий Витальевич ЧАБАН
>
>
> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote:
> > Hi.
> >
> > Is it a good idea to mimic
Following up on fluctuations and ensembles:
The following paper discusses tests of whether an ensemble has the correct
distribution of energies, including fluctuations of all scale:
"Simple quantitative tests to validate sampling from thermodynamic
ensembles"
http://pubs.acs.org/doi/abs/10.1021/c
what is it needed for?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote:
> Hi.
>
> Is it a good idea to mimic NVE by a NVT simulation with a large temperature
> coupling time constant, to reduce the effect of the thermostat ?
>
> If I use V-resca
On Fri, 10 Oct 2014, Mark Abraham wrote:
On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote:
Hi.
Is it a good idea to mimic NVE by a NVT simulation with a large temperature
coupling time constant, to reduce the effect of the thermostat ?
Not if your observable is the total energy. But for m
On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote:
> Hi.
>
> Is it a good idea to mimic NVE by a NVT simulation with a large temperature
> coupling time constant, to reduce the effect of the thermostat ?
>
Not if your observable is the total energy. But for most interesting
observables, this is m
seems to be a good idea, as the "canonical sampling through velocity
rescaling" paper by G.Bussi said.
arxiv.org/pdf/0803.4060
On Fri, Oct 10, 2014 at 1:41 PM, Johnny Lu wrote:
> Hi.
>
> Is it a good idea to mimic NVE by a NVT simulation with a large
> temperature coupling time constant, to red
Hi.
Is it a good idea to mimic NVE by a NVT simulation with a large temperature
coupling time constant, to reduce the effect of the thermostat ?
If I use V-rescale thermostat, what artifacts will the simulation get if I
use a large coupling time (say, 500 ps) and single precision gromacs ?
Thank
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