Re: Espressomd-users Digest, Vol 110, Issue 4

[Raghvendra Singh]

Thank you Jean-Noel, 
The explanation is clear and sound, but I am interested in colloid potential 
functions. as provided in example:
from visualization_charged.py
# FORCE FIELDS
species = ["Cl", "Na", "Colloid", "Solvent"]
types = {"Cl": 0, "Na": 1, "Colloid": 2, "Solvent": 3}
charges = {"Cl": -1.0, "Na": 1.0, "Colloid": -3.0, "Solvent": 0.0}
lj_sigmas = {"Cl": 3.85, "Na": 2.52, "Colloid": 10.0, "Solvent": 1.5}
lj_epsilons = {"Cl": 192.45, "Na": 17.44,
               "Colloid": 100.0, "Solvent": 50.0}
lj_cuts = {"Cl": 2.0 * lj_sigmas["Cl"], "Na": 2.0 * lj_sigmas["Na"],
           "Colloid": 1.5 * lj_sigmas["Colloid"], "Solvent": 2.0 * 
lj_sigmas["Solvent"]}
masses = {"Cl": 35.453, "Na": 22.99, "Colloid": 300, "Solvent": 18.0}

I get that the properties defined here for NaCl are well documented LJ-pair 
potentials, 
but for the above mentioned "colloid", how are the properties calculated??

as in my case I would like to simulate the spherical colloidal particle (not 
the raspberry model) of 100-500nm in implicit solvent and in real units 
(distance= in angstrom, energy=kJ/mol etc..)
is there a way in espresso I can calculte such properties providing the 
particle diameter, cutoff radius and mass etc.

Thank you

Best
Raghav 


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Subject: Espressomd-users Digest, Vol 110, Issue 4

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Today's Topics:

   1. Units of sigma and epsilon (Raghvendra Singh)
   2. Re: Units of sigma and epsilon (=?UTF-8?Q?Jean-No=c3=abl_Grad?=)


----------------------------------------------------------------------

Message: 1
Date: Mon, 9 Mar 2020 11:02:15 +0100 (CET)
From: Raghvendra Singh <address@hidden>
To: address@hidden
Subject: Units of sigma and epsilon
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset=utf-8

Dear EspressoMD users,

I have been trying some examples from espressmd sample directory and would like 
to know what are the units of sigma and epsilon in the visualization_charged.py 
script for colloids.
I am planning to run simulations on large colloidal particle of diameters 
ranging from 100-500nm.
if someone can provide me details regarding the unit system used in the 
visualization_charged.py then I can adapt to the unit system with parameters 
for large colloidal particles.

if someone can help me out regarding parametrization of large colloidal 
particle (not the raspberry model but simple point particle of LJ-kind).

Thanking you

Best
Raghav



------------------------------

Message: 2
Date: Mon, 9 Mar 2020 11:21:11 +0100
From: "=?UTF-8?Q?Jean-No=c3=abl_Grad?=" <address@hidden>
To: address@hidden
Subject: Re: Units of sigma and epsilon
Message-ID:
        <address@hidden>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear Raghav,

The unit system is taken from Fuentes-Azcatl and Barbosa 2016 
(https://doi.org/10.1021/acs.jpcb.5b12584). Sigmas are in Angstroms, 
epsilons in kbT. You'll find more details in tutorial 02 part 1 section 
6 
(http://espressomd.org/html/tutorials_html/02-charged_system/02-charged_system-1.html#6-Task---Real-Units)
 
and its solutions scripts for the P3M method or in tutorial 02 part 2 
(http://espressomd.org/html/tutorials_html/02-charged_system/02-charged_system-2.html)
 
for the ELC method. The paper shows how this NaCl forcefield was 
parameterized and validated.

Best,
JN

On 3/9/20 11:02 AM, Raghvendra Singh wrote:
> Dear EspressoMD users,
> 
> I have been trying some examples from espressmd sample directory and would 
> like to know what are the units of sigma and epsilon in the 
> visualization_charged.py script for colloids.
> I am planning to run simulations on large colloidal particle of diameters 
> ranging from 100-500nm.
> if someone can provide me details regarding the unit system used in the 
> visualization_charged.py then I can adapt to the unit system with parameters 
> for large colloidal particles.
> 
> if someone can help me out regarding parametrization of large colloidal 
> particle (not the raspberry model but simple point particle of LJ-kind).
> 
> Thanking you
> 
> Best
> Raghav
> 



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