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

From: Dr. Jens Smiatek
Subject: Re: [ESPResSo-users] interface between VOTCA and ESPResSo
Date: Wed, 19 Jun 2013 22:04:53 +0200
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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,

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;  ;                              Zhicheng Guo

Dr. Jens Smiatek

Institute for Computational Physics
University of Stuttgart
Allmandring 3
70569 Stuttgart

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