You need some ions to neutralise the system for long range electrostatics to
work. We usually add more to make the simulation more like the real system
(solution or cell).
> On Jan 21, 2018, at 1:12 AM, Sankaran SV . <119013...@sastra.ac.in> wrote:
>
> Dear all,
>
>I am a beginer.
Thanks Justin. It’s two protein chains, water and NaCl but there are virtual
sites and CMAP (charmm27 ff). I generated the full topology with grompp so yes
please could I try your script. Would CHARMM-GUI or VMD be able to generate the
CMAP?
Best wishes
James
> On Jan 11, 2018, at 8:08 AM, J
Hi,
Does anyone have any experience with creating a psf file from a gromacs
topology? I have a collaborator who uses NAMD and they are going to analyse
some of my gromacs simulations together with some of their simulations but need
psf files to do that.
Many thanks and best wishes
James
--
G