Dear experts,
I have a Coarse-grained simulation system where a dimer peptide is situated
on the surface of the lipid bilayer. Can anyone help me to solve the PBC
effect, I have tried with pbc mol, cluster and centring.
Here is the link for 200 frames and starting configuration.
Thanks in
Make the selection based on the atomtype and resname
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
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When the only
Hi,
As you see in the docs
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-refcoord-scaling
there are different reference coordinates chosen on your two fragments. The
2018 series of GROMACS prompts you to choose what those coordinates are
with grompp -r, which
Hi Dr. Mark
I have already posted in the respective forum. I am just looking for some
alternative method or to know if I am doing it wrong.!
But anyway I overcame this error.
After docking, add respective hydrogens and save it as mol2 file. Make it
as complex with protein and save as PDB. These
Dear Gromacs Users,
I'm performing MD simulations (NPT) with position restraints for part
of the system, thereby using the refcoord-scaling=com option in the
mdp-file. After the MD run has finished and I'm restarting the MD by
taking the last frame and simply extending the simulation time,
Den 2018-08-11 kl. 16:33, skrev Chi Yuen Pak:
Dear GROMACS users,
I would like to ask a question concerning about the simulation of a water
droplet, with SWM4-DP polarizable water model in nonperiodic boundary
conditions. The GROMACS version I use is 2018.2. I have been only able to
