Hello all,
I have two questions.
1. Is there a tool to convert LAMMPS data file to gromacs topology file. I
am using GAFF forcefield.
Test particle insertion:
In the manual it is mentioned that "This trajectory should not contain the
molecule to be inserted."
If I want to estimate excess chem
Hello all
I was going through tpi.cpp file in the latest version of gromacs.
I found this flag
"TPI does not work (yet) with the Verlet cut-off scheme"
My question:
Does test particle insertion use the group cut off scheme to calculate the
change in energy ? (assuming equilibrium trajectories
up cutoff scheme. But the impact of
> that difference is nearly zero.
>
> Mark
>
> On Sat, Mar 3, 2018, 22:29 Arun Srikanth wrote:
>
> > Hello all
> >
> > I was going through tpi.cpp file in the latest version of gromacs.
> >
> > I found this flag
ch case the all the atoms belonging to one
> monomer
> > can be considered a charged group.
> >
> >
> >
> > Thank you again
> > Arun
> >
> >
> >
> > On Sat, Mar 3, 2018 at 5:44 PM, Mark Abraham
> > wrote:
> >
> > &
Hi if you have rdf it is easy to calculate the coordination number by
numerical integration
https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions
Arun
On Mon, Nov 26, 2018 at 11:38 AM Maria Luisa wrote:
> Dear users,
> I need to calculate rdf coordination number over
Unless you give you give details how you calculate the MSD it will not be
possible to help.
Are you using unwrapped co-ordinates in your calculations for MSD?
Arun
On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani wrote:
> Hi,
> I am trying to post-processing my results and calculate MSD (mean square
Are you simulating a crystal or amorphous system?
Arun
On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal
wrote:
> 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
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,
> Mohamed