[gmx-users] Question on gmx editconf, pbc and NPT

[Dallas Warren]

Pressure coupling is explained here ->
http://manual.gromacs.org/documentation/current/reference-manual/algorithms/molecular-dynamics.html#pressure-coupling

There is no pressure applied to the face of a simulation box, as the face
of the simulation box itself is an arbitrary construct done to allow us to
visualise the system.  The particle coordinates and box vectors are what is
adjusted to maintain the pressure.

Sounds more like you want to use this
http://manual.gromacs.org/documentation/current/reference-manual/special/pulling.html#the-pull-code

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 27 Dec 2018 at 22:14, Sebastian Muraru <
sebastian.muraru at grabtop.upb.ro> wrote:

> Hi there! Please help me figure something out.
>
> I have a setup made out of two molecules and I would like to investigate
> when happens when they meet (graphene + biomolecule). One of them is fixed
> by position restraints, one of them is mobile. When running a simulation
> under NPT conditions I assumed pressure is applied so that everything is
> 'slightly guided' towards the center of the simulation box (given a high
> enough pressure value). Would that assumption be correct? Or is pressure
> presumably applied on the faces of the simulation box?
>
> Thus, I figured, since I want to check what happens when the molecules
> meet, I want molecule_1 to be in the center of the simulation box and have
> molecule_2 slightly guided towards it. However, given that the distance
> between the molecules is known and fixed, placing the box so that
> molecule_1 is at the center leaves a part of molecule_2 out of the box
> through the top face.
>
> I assumed this would not be a problem during a simulation due to pbc being
> on, thus allowing the part of molecule_2 that's out of the box to reenter
> through the bottom layer. However, I also need to go through a solvation
> step and that I think this complicates things because a part of molecule_2
> will not be in solvent. Would you know a workaround for this issue? I try
> to avoid making the box taller / bigger.
>
> Thanks and a Happy Upcoming New Year to the Gromacs Community!
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