[gmx-users] Dissipative Particle Dynamics (DPD)

[David van der Spoel]

Suman Chakrabarty wrote:
>    Dear Tsjerk,
> 
> thanks for your response. It makes sense.
> 
> Once I am through with my current project that I am busy with, I might 
> take up this implementation more seriously and actively. By that time I 
> need to be in a position to be able to look into the Gromacs source code 
> and understand how everything works. That would be an interesting 
> project in itself! :)
> 
> For the time being I am in urgent need of an already implemented package 
> and may be I'd go look into LAMMPS for help.

As far as I know most of this stuff is being worked on by Berk Hess.
In standard GROMACS you can use tabulated potentials for everything 
bonded and non-bonded, if that helps overcome the harmonic-only problem.
> 
> 
> Best regards,
> Suman.
> 
> 
> Tsjerk Wassenaar wrote:
>> Hi Suman,
>>
>> I think this discussion would be better placed on the developers-list
>> (but I'm not sure you're subscribed to that so I'll keep it here).
>> First, I think it's not a good idea (and it's against Gromacs
>> philosophy) to remove functionality, as this will disallow repeating
>> earlier studies.
>> Second, it may be a good idea to implement DPD, but you'll either have
>> to wait until one of the developers feels like implementing it, needs
>> it for it's own research or you'll have to take up the effort to write
>> an implementation, which can then (if approved of) be added to the
>> main version. Each of the developers has its own research projects and
>> it hardly ever works just asking something you need to be implemented,
>> without providing the implementation.
>>
>> Maybe a bit disappointing, sorry.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Tue, Sep 2, 2008 at 7:39 AM, Suman Chakrabarty
>> <suman at sscu.iisc.ernet.in> <mailto:suman at sscu.iisc.ernet.in> wrote:
>>   
>>> Yang Ye wrote:
>>>
>>> there is dpdmacs available..
>>>
>>> Yes, I know. But that seems to support only harmonic potential for even
>>> non-bonded interaction (DPD manual page 4-5), which is rather unphysical and
>>> not suitable for my purpose.
>>>
>>>
>>>
>>> Regards,
>>> Suman Chakrabarty.
>>>
>>>     
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se