Dear lammps users,
I simulate polyelectrolyte phase separation in the implicit solvent. My model consists of 7 beads and equilibrium bond length is 5.6 A with harmonic bond having bond oscillation constant 350kcal/mol/A^2. All beads are charged.
What I want to know is…
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I am considering implicit solvent just incoporating dielectric constant as 80, which is for the case of water. In this case, if I use “fix npt” for the NPT ensemble simulation, is it really running the simulation under the implicit solvent? Most of the papers run implicit solvent simulation using langevin thermostat…
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Is there a way that I can run NPT ensemble by using langevin thermostat?
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I have come to know that “Mark s
Stevense” is really famous for the coarse-grained polyelectrolyte. Can you suggest me references that I can refer to? I heard hist paper published 20 years ago explained everything about the coarse-graining of the polyelectrolyte but I couldn’t find which one is original.
Please kindly give me a hand…
With my best regards
Dear lammps users,
I simulate polyelectrolyte phase separation in the implicit solvent. My model consists of 7 beads and equilibrium bond length is 5.6 A with harmonic bond having bond oscillation constant 350kcal/mol/A^2. All beads are charged.
What I want to know is…
- I am considering implicit solvent just incoporating dielectric constant as 80, which is for the case of water. In this case, if I use “fix npt” for the NPT ensemble simulation, is it really running the simulation under the implicit solvent? Most of the papers run implicit solvent simulation using langevin thermostat…
a langevin thermostat is a very minimal model for an implicit solvent. you have to choose your damping time very carefully to represent the viscosity of the solvent.
when used for regular thermostatting, the time constant is usually chosen to be very large so the thermostat does only very minimally interact with the system, just enough to maintain the desired temperature without impacting the trajectories too much.
mind you, fix langevin is only one out of multiple langevin-like thermostats in LAMMPS.
- Is there a way that I can run NPT ensemble by using langevin thermostat?
you could use fix nph in combination with fix langevin if you want to combine a nose-hoover barostat with a langevin thermostat.
or you could use the combination of fix nve, fix langevin and fix press/berendsen
axel.