I answered this the other day:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-September/115865.html
-Justin
On 9/14/17 9:55 AM, Agatha Faria wrote:
Dear GROMACS Community,
I am very new with GROMACS I am trying to run a simulation of an ionic liquid
> Dear GROMACS Community,
>
> I am very new with GROMACS I am trying to run a simulation of an ionic liquid
> (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to the
> following protocol:
>
> 1. Prepared the respective PDB files and added/modified the OPLS/AA force
> field
On 9/13/17 5:55 PM, Agatha Faria wrote:
Dear GROMACS Community,
I am very new with GROMACS I am trying to run a simulation of an ionic
liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate)
according to the following protocol:
1. Prepared the respective PDB files and added/modified
Dear GROMACS Community,
I am very new with GROMACS I am trying to run a simulation of an ionic liquid
(1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to the
following protocol:
1. Prepared the respective PDB files and added/modified the OPLS/AA force field
parameters
Hi Ghosh,
Thanks for your answer.
But I'm not sure if I understood what you meant.
I already used insert-molecules command to create a box with the cationic
species.
Now, should I use the same command to include the anionic species into the
box?
Best
*Prof. Dr. Ednilsom OrestesDepartamento de
On 9/5/17 2:32 PM, Ednilsom Orestes wrote:
Dear GROMACS Community,
I am very new with GROMACS I am trying to run a simulation of an ionic
liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to
the following protocol:
1. Prepared the respective PDB files and added/modified
Hi,
I am not sure why you used the gmx solvate command for putting the
anionic species in your simulation box. It is meant for filling up the
simulation box with water molceules as the resname 'SOL' in the
topol.top file. Thus when you hit grompp it expects 'SOL' entry in
your topology file, cant
Dear GROMACS Community,
I am very new with GROMACS I am trying to run a simulation of an ionic
liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to
the following protocol:
1. Prepared the respective PDB files and added/modified the OPLS/AA force
field parameters updating
