Dear users,
I know interaction energy calculation is carried out via energygrps setting
in mdp file.
Because free energy-related settings do not include this energygrps
setting, so I think this energygrps setting may NOT be related to free
energy settings.
Could I ask whether my idea is correct
Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal:
Hello everybody,
I have two fundamental questions please.
I have measured the fee volume and I discovered that, the free volume
changes with respect to the time during the production run (different value
for each frame). However I have measured
Is it an NPT simulation or NVT simulation?
Arun
On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal,
wrote:
> Yes I measured both, the density and the free volume using gromacs.
>
> Since the free volume changes with respect to time, shouldn’t the density
> also change with time ?
>
> Thanks,
>
Yes I measured both, the density and the free volume using gromacs.
Since the free volume changes with respect to time, shouldn’t the density
also change with time ?
Thanks,
Mohamed
On Wed, May 6, 2020 at 08:23 David van der Spoel
wrote:
> Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal:
> >
I started with NVT then NPT then md production run.
Thanks,
Kohamed
On Wed, May 6, 2020 at 10:40 Arun Srikanth wrote:
> Is it an NPT simulation or NVT simulation?
> Arun
>
> On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal,
> wrote:
>
> > Yes I measured both, the density and the free volume using
Den 2020-05-06 kl. 10:21, skrev Mohamed Abdelaal:
Yes I measured both, the density and the free volume using gromacs.
Since the free volume changes with respect to time, shouldn’t the density
also change with time ?
What do you mean with "changes"? If the density is constant (with
Dear Gromacs users,
I am interested on studying the interaction between large metal cluster
anions (polyoxometallates, POM) with different organic cations (e.g
perylenes, etc..) in water.
I have already the non bonded parameters of POMs from literature, while the
bonded parameters I calculated