Steered method Lammps

Dear all,

I am trying to calculate the PMF between silice surface and graphene of a system composed of silice mineral, graphene and water by molecular dynamics. For this, I am using the Steered method in couple and the constant velocity method in Lammps. I would like to understand what is the difference between using negative velocity and negative force constate:

fix 1 Silica smd smd cvel -2 2.4e-4 couple G NULL NULL auto 0.0
fix 1 Silice smd cvel 2 -2.4e-4 couple G NULL NULL auto 0.0

I have made a test with a simple system composed by two simple atoms without charge and joined by the Lennard-jones potential in a NVE assembly, I have verified that both are a stretching process but in the first one the internal coordinate is increasing and in the second one it is decreasing, but in both, as long as the distance between the coupled groups and the internal coordinate is negative, the force applied by the spring pushes them.

So, how can this affect the PMF and what is the most advisable?



The sign of the velocity determines the pull direction, i.e. either toward the reference point or away from it. The sign of the force constant determined whether there is a restrain to keep the atoms in the fix group near the target point or to move them away from it. Basically it will turn the harmonic potential function upside down and thus makes no sense at all for this kind of method.

It is good that you are making tests, but the test you chose and how you look at it does not say much. You need to make additional tests where a few additional atoms are present (e.g. by preference immobile atoms and located near the push/pull path, so that the steered MD target atom has to pass them and thus there will be some force related to the push/pull path imposed by fix smd.

Dr. Axel,

It is interesting to understand how a change in the spring constant could change the internal coordinate and the surface potential energy.

I have another question. Using the following line to calculate the PMF and constrain the motion of the atoms to be relative to the centre of mass of the Silice, in the system composed of Silice, Graphene (G) and Water:

fix 1 Silice smd cvel 2 -2.4e-4 couple G NULL NULL auto 0.0
fix 9 Silice recenter INIT INIT INIT INIT units box shift all

I could calculate with few variables the distance between the centres of mass of the Silice and the Graphene groups on the Z axis. Then, I could calculate the relative acceleration of Graphene with respect to the centre of mass of Silicon on the Z-axis using a numerical method, and find out the force exerted on the centre of mass of Graphene by both groups Silice and Water, basically by multiplying the mass of Graphene by the acceleration and adding the spring force. Is this correct?



I don’t think it is “interesting”. It just looks like it has some hidden meaning only because of the simplicity of your test system. For the most part, using a negative force constant in this context (like for a harmonic bond or angle) makes no sense at all and renders the simulation bogus. LAMMPS will still compute forces and move atoms, but the point of a harmonic potential is to pull atoms back to the center the further they are away and not to push them away more when they are further away.

You are moving this away from a discussion about LAMMPS to a discussion about free energy calculations. That is not something that is relevant for this forum or I would have an interest to discuss. This is a topic for you to learn from text books and then discuss with your adviser(s), tutor(s), and peer(s). If you think some other person that is member of the forum would want to discuss with you, you can post in the “Science Talk” category, that was created for such purposes.