Hi and
Happy new year to everybody,
First of all, thank you very much for your previous answers.
I understood from the Espresso manual that the force is, as you
say, U'(r)/r being the r the distance between two beads in the
case of tabulated nonbonded potentials. However, in the case of
tabulated angle potentials I am not be able to understand the
meaning of r. Which is the r that I have to use?. Is the
connecting distance between 12 beads? or 13 beads??? (for the
angle between (1)(2)(3) beads)
Best regards,
Javi
Hi!
On Thursday 15 December 2011 10:40:15 Javier Ramos wrote:
> Dear Espresso users,
>
> I am trying to use a tabulated angle potential (variant 2 in the section
> 5.3.7 of the user guide). I have two questions.
>
> i) Does the angle potetial zero corresponds to the polymer is this
> position: (p1)(p2)(p3)?
Yes, if you mean the stretched position, where all particles are in a line.
> ii) It is not clear for me which is the scaled length that I need to
> use for the forces. Following the explanation in the nonbonded
> tabulated potential I am assuming that the second column has to be built
> as F(theta) =  Vprime(theta) / theta where Vprime is the derivate of
> V(theta) respect to theta and theta is the angle between p1,p2 and p3
> particles. is that right?
According to the User's guide, no. It says only that the forces are scaled
with the inverse length of the connecting vectors, which is what is required
due to the angle. What you therefore give is the magnitude of the force on one
of the two outer particles, multiplied by the distance of the particle to the
center particle.
Axel

JP Dr. Axel Arnold
ICP, Universität Stuttgart
Pfaffenwaldring 27
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609


Dr. Javier Ramos
Molecular Structure and Properties of Polymers
Department of Macromolecular Physics
Instituto de Estructura de la Materia (CSIC)
C/ Serrano 113 bis 28006 Madrid (Spain)
Voice +34 91 561 68 00 (943112)
Fax +34 91 585 54 13
http://www.biophym.iem.csic.es/biophym

