On 8/1/15 6:38 PM, 折晓会 wrote:
Thank you Professor Justin for your reply!
The .mdp files for energy minimization and equilibration are shown in the
following. During the energy minimization, the simulation stops at step=38,
which may be unreasonable. The initial configuration of the system is s
On 8/1/15 7:08 PM, sujithkakkat . wrote:
Dear Justin,
I am following your tutorial about CO2 topology using virtual sites.
I find that in the topology provided, you have not reassigned the particle
type as virtual (V) for the C and O atoms (which are treated as the virtual
sites in the model)
Dear Justin,
I am following your tutorial about CO2 topology using virtual sites.
I find that in the topology provided, you have not reassigned the particle
type as virtual (V) for the C and O atoms (which are treated as the virtual
sites in the model). Instead, they are directly selected from th
Thank you Professor Justin for your reply!
The .mdp files for energy minimization and equilibration are shown in the
following. During the energy minimization, the simulation stops at step=38,
which may be unreasonable. The initial configuration of the system is simple
cubic. The drude particl
You need to provide path to the DFTB+ executable and specify the MM
part in gromacs.
Take care of versions of both codes!
On Sat, Aug 1, 2015 at 3:01 AM, Zhenyu Meng wrote:
> Hi Justin,
> I read the manual and it mentions how to specify QM/MM parameters, but no
> detail is provided. Also it sa
Dear Justin,
I am following your tutorial about CO2 topology using virtual sites.
I find that in the topology provided, you have not reassigned the particle
type as virtual (V) for the C and O atoms (which are treated as the virtual
sites in the model). Instead, they are directly selected from th
