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Re: [ESPResSo-users] interface between VOTCA and ESPResSo

From: Christoph Junghans
Subject: Re: [ESPResSo-users] interface between VOTCA and ESPResSo
Date: Wed, 19 Jun 2013 14:57:31 -0600

2013/6/19 Dr. Jens Smiatek <address@hidden>:
> Dear Zhicheng,
> as far as I know is the Votca-mapping related to potential of mean forces,
> or in other words conservative interaction parameters like Lennard-Jones
> variables and tabulated potentials to derive a systematic coarse-graining.
> For example, you map the radial distribution function of the molecular
> center of mass to Lennard-Jones parameters (often not possible) or to
> tabulated interaction potentials.
> The parameters of the DPD thermostat are related to intrinsic system
> properties like the shear viscosity (gamma_DPD, r_cut) or the self diffusion
> coefficient.
> There are no conservative interactions in the command you have shown.
> For the systematic matching of these parameters (shear viscosity, self
> diffusion coefficients, etc.) you have to use a more heuristic matching
> scheme if otherwise not possible.
> Best regards,
> Jens

Hi Zhicheng,

Jens is right, VOTCA can only help you determining the conservative
part of the interaction. And inter_dpd is only the stochastic part of
the DPD interaction.
The stochastic interaction can only be used to assure you have NVT
ensemble (parameter gamma) and to tweak the dynamic properties
(parameter tgamma)

For most systems, gamma has no influence on the dynamics of the system:
but tgamma has an influence:


> On 06/19/2013 04:57 AM, guozhicheng222 wrote:
> Dear all:
> I construct a energy material system(RDX: C3N6O6H6) containing 800 RDX
> molecules to map onto the coarse-grained beads by VOTCA for the input of
> ESPResSo. However, the method of mapping the interaction parameter is a
> challenge. For our system (a bead "A" represent a RDX molecule), in order to
> describe the interaction of beads, we used the dpd (dissipative particle
> dynamics) interaction within ESPResSo. The relative command lines just like:
>                                               inter 0 0 inter_dpd gamma
> r_cut wf tgamma tr_cut twf
> the number 0 means the bead type(A), gamma, r_cut, wf, tgamma, tr_cut, and
> twf represent the parameter of dpd interaction. Therefore, how can I obtain
> these parameters based on the coarse-grained model in VOTCA. Thanks for
> anyone's help.
> Best Regards!
> &n bsp;&nbsp ;                              Zhicheng Guo
> 来自网易手机号码邮箱了解更多
> --
> ================
> Dr. Jens Smiatek
> Institute for Computational Physics
> University of Stuttgart
> Allmandring 3
> 70569 Stuttgart
> Germany
> Office: 1.032
> Phone: +49-(0)711/685 63757
> E-Mail: address@hidden

Christoph Junghans

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