> I think you don`t need to build topology separately. Using appropriate
force field will do. For protein-DNA simulation amber99sb works well.
Amber99bsc1.ff is a new module available for gromacs users. You may use
them or it is always better to refer literature to use the more
appropriate forcefei
Hello Gromacs experts,
First things first, I apologize for any double post but I just
joined the community so I'm very new and only found 1-2 posts related to my
problem but the solutions did not work. I have been doing MD for about
6-months using NAMD but want to also try out Gromacs. T
Check the literature to see what others that are simulating similar
molecules are using and looking to study similar "things" (energies,
structures etc) that you are.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
Hi,
I am running some MD simulation using position restraints and turning-off
centre of mass removal (comm-mode = None in the .mdp file).
However, GROMACS 2020 still tell me with a note that 'removing center of mass
motion in the presence of position restraints might cause artifacts'.
So, is
The "gmx mindist?? command can output the number of contacts (numcont) between
two groups as a function of time. Is there a way to only consider the native
contacts, without using the PLUMED?
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I am new in the field of molecular dynamics and simulation. I am trying to
learn online tutorial for gromacs. I have docked my DNA with protein in
HADDOCK. I want to run a simulation in gromacs. Can I make topology file of
the complex together or I need to make topology file separately. Which
force
@Justin: the lipid is not yet added to the charmm directory. Any
script?@Michele: pdb2gmx only works for proteins.-YogeshSent using Zoho
Mail On Mon, 27 Jan 2020 19:34:34 +0530 Justin Lemkul
wrote On 1/27/20 4:51 AM, atb files wrote:> >>
