Dear all:
Thanks a lot for your suggestion. It seems that I have to understand the dpd interaction further.
Best Wishes!
Zhicheng
At 2013-06-21 00:00:21,address@hidden wrote:
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> 1. Re: interface between VOTCA and ESPResSo (Christoph Junghans)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 19 Jun 2013 14:57:31 -0600
>From: Christoph Junghans <address@hidden>
>To: "Dr. Jens Smiatek" <address@hidden>
>Cc: address@hidden
>Subject: Re: [ESPResSo-users] interface between VOTCA and ESPResSo
>Message-ID:
> <address@hidden>
>Content-Type: text/plain; charset=GB2312
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>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:
><http://link.aps.org/doi/10.1103/PhysRevE.68.046702>
>but tgamma has an influence:
><http://dx.doi.org/10.1039/b713568h>
>
>Cheers,
>
>Christoph
>>
>>
>>
>> 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
>> Germany
>>
>> Office: 1.032
>> Phone: +49-(0)711/685 63757
>> E-Mail: address@hidden
>
>
>
>--
>Christoph Junghans
>Web: http://www.compphys.de
>
>
>
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