Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

c .edr files generated using mpirun > (Abhishek Acharya) > 6. Grid Spacing (Apramita Chand) > > >-- > >Message: 1 >Date: Mon, 03 Jul 2017 00:03:52 + >From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org >

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Sure - one should use a tool capable of doing the job, and use its optional capabilities accordingly. Choosing non-bonded exclusions based on bonds, in a way that does not implement the intended model physics, is indeed wrong, but that doesn't make the use of modified 1-4 pair interactions

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Hi, On Fri, Jun 30, 2017 at 2:46 AM Alex wrote: > > > > > >> > >> He he, childish :) > > > > David, no offense intended. I just think that when applied to solids, the > entire concept of what works so well for biomolecular systems becomes a bit > of a joke. And vice versa,

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

bove experiment first. > >Mark > >On Fri, Jun 30, 2017 at 12:21 AM Thanh Le <thanh.q...@sjsu.edu> wrote: > >> Hi Mr. Abraham. >> My system is quite small, only about 8000 atoms. I have run this system >> for 100 ns, which took roughly about 2 days. Hence, a ru

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

> > >> >> He he, childish :) > > David, no offense intended. I just think that when applied to solids, the entire concept of what works so well for biomolecular systems becomes a bit of a joke. And vice versa, to be fair. Spoken from experience, really -- we here used Gromacs to simulate things

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

On 28/06/17 20:22, Alex wrote: This community is mostly focused on other things. If you have solid silica under a non-native (to Gromacs) forcefield and all the bonded parameters have been copied correctly, there may be issues with your partial charges, LJ parameters, and mixing rules. Also make

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

This community is mostly focused on other things. If you have solid silica under a non-native (to Gromacs) forcefield and all the bonded parameters have been copied correctly, there may be issues with your partial charges, LJ parameters, and mixing rules. Also make sure your original

[gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Hi, I converted the InterfaceFF silica parameters to use in Gromacs (and to be compatible with the AMBER forcefield) and have gotten some problems, namely I am getting a slightly bigger equilibrium bond length than I should. I was wondering if there were other Gromacs users out there that have