[gmx-users] Two questions: LAMMPS to gromacs, Test particle insertion

2017-11-21 Thread Arun Srikanth
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

Re: [gmx-users] Test particle insertion change in energy - group cut off scheme

2018-03-03 Thread Arun Srikanth
gt; > Mark > > On Sun, Mar 4, 2018, 00:18 Arun Srikanth <askfora...@gmail.com> wrote: > > > Thank you. > > > > Can you please elaborate on this or clarify the following questions? > > > > 1. Supposing I have inserted one water molecule

Re: [gmx-users] Test particle insertion change in energy - group cut off scheme

2018-03-03 Thread Arun Srikanth
will only work if you choose the group cutoff scheme. But the impact of > that difference is nearly zero. > > Mark > > On Sat, Mar 3, 2018, 22:29 Arun Srikanth <askfora...@gmail.com> wrote: > > > Hello all > > > > I was going through tpi.cpp file in the latest v

[gmx-users] Test particle insertion change in energy - group cut off scheme

2018-03-03 Thread Arun Srikanth
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

Re: [gmx-users] rdf coordination number over time (ns)

2018-11-26 Thread Arun Srikanth
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

Re: [gmx-users] Question about Mean Square Displacement (MSD)

2020-04-18 Thread Arun Srikanth
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

Re: [gmx-users] Free volume variation during the simulation

2020-05-05 Thread Arun Srikanth
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

Re: [gmx-users] Free volume variation during the simulation

2020-05-06 Thread Arun Srikanth
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, >