Hi,

I want to do pmf (potential mean force) calculation for my system , is there any direct command to calculate pmf in lammps. So that i can avoid Umbrella sampling

for pmf calculation. I will be very thankful for yours kind help.

Thanks in advance…

With Regards,

Pooja Sahu

Hi,

I want to do pmf (potential mean force) calculation for my system , is

there any direct command to calculate pmf in lammps. So that i can avoid

Umbrella sampling for pmf calculation. I will be very thankful for yours kind help.

what is the problem with umbrella sampling?

in combination with WHAM it is in many

cases the best way to compute a PMF.

what do you need the PMF for?

there are alternative approaches

like steered MD or metadynamics

or adaptive biasing force calculations.

there are multiple options to do those in lammps

axel.

PMF is related to the radial distribution function. So, the easiest

way to calculate PMF is calculate the RDF and then calculate PMF from

w(r) = - k_BT * log(g(r)).

This algorithmic relationship between the PMF and the RDF means that a

relatively small change in the free energy (i.e. a small multiple of

k_BT) may correspond to g(r) changing by an order of magnitude from

its most likely value.

Hope this helps

Hi,

A great thanks for the kind help, but i have one more doubt. Actually I want to calculate pmf to get binding energy of ion with crown-ether in presence as well as absence of water. I am new to simulation, till now i have calculated rdf between two types atoms only. Here, should i use center of mass of crown ether to calculate rdf with ion. will it give binding energy?

Thanks in advance…

now, this is a rather different question. binding energy and PMF are

different. To calculate binding energy between crown ether and ion,

you have to consider all Oxygen atoms which are bound to the ion, I

don't think the CG of the ether can be used to calculate BE (refer to

crown ether structure).

If you want just a quick PMF calculation, calculate the RDF between O

atoms and the ion and PMF from the formula.

PMF is related to the radial distribution function. So, the easiest

way to calculate PMF is calculate the RDF and then calculate PMF from

w(r) = - k_BT * log(g(r)).

that is a very special case (and only works well for dilute monoatomic gases).

there are many other PMFs that people calculate.

axel.

now, this is a rather different question. binding energy and PMF are

different. To calculate binding energy between crown ether and ion,

not at all. the binding free energy for a _one dimensional

reaction coordinate_ is the integral over the PMF.

you have to consider all Oxygen atoms which are bound to the ion, I

don't think the CG of the ether can be used to calculate BE (refer to

crown ether structure).

If you want just a quick PMF calculation, calculate the RDF between O

atoms and the ion and PMF from the formula.

sorry, but this is not good advice. see my other response.

actually, umbrella sampling, steered MD or metadynamics

(the latter with a suitably chosen reaction coordinate)

are the best ways to get this.

axel.

Hi,

A great thanks for the kind help, but i have one more doubt. Actually I

want to calculate pmf to get binding energy of ion with crown-ether in

presence as well as absence of water. I am new to simulation, till now i

have calculated rdf between two types atoms only. Here, should i use center

of mass of crown ether to calculate rdf with ion. will it give binding

energy?

it doesn't. as i mentioned earlier, the relation between

g(r) and PMF cannot be applied here.

you still didn't explain, why umbrella

sampling would be a bad choice?

it gives you the best control over accuracy

and convergence and is embarrassingly

parallel and thus can be run very efficiently

on a parallel machine.

the next best choice would be to run a trajectory

of the bound state and store away a set of restarts

and then run a bunch of steered MD trajectories

where you use a center-of-mass distance collective

variable (using the USER-COLVARS package, or

fix smd) and average over them.

of course, metadynamics (via USER-COLVARS

or the external PLUMED code) can also be used.

using USER-COLVARS has the advantage that you

can use the same interface for umbrella sampling,

SMD and MTD. however, i just got a bug report for

the code that is in the current LAMMPS release

and sent out a patch with a bug fix to steve. so

you'd have to use either LAMMPS-ICMS for now

or wait until steve has incorporated the patch.

please also note, that any of these accelerated

sampling techniques require that you spend some

effort learning how they work and how you use

them correctly.

axel.