[gmx-users] Dissipative Particle Dynamics (DPD)
David van der Spoel
spoel at xray.bmc.uu.se
Tue Sep 2 09:38:28 CEST 2008
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,
> 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.
>> 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.
>>> Suman Chakrabarty.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users