Re: [gmx-users] Dissipative Particle Dynamics (DPD)

2008-09-02 Thread David van der Spoel
Ran Friedman wrote: 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. In which version are tabulated potentials available? non-bonded

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

2008-09-02 Thread Ran Friedman
> 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. In which version are tabulated potentials available? Thanks, Ran ___

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

2008-09-02 Thread 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

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

2008-09-02 Thread Suman Chakrabarty
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 everyth

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

2008-09-02 Thread Tsjerk Wassenaar
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. Sec

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

2008-09-01 Thread Suman Chakrabarty
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. __

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

2008-09-01 Thread Yang Ye
there is dpdmacs available.. Regards, Yang Ye - Original Message From: Suman Chakrabarty <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, September 1, 2008 5:50:15 PM Subject: [gmx-users] Dissipative Particle Dynamics (DPD) Dear all, since one of my

[gmx-users] Dissipative Particle Dynamics (DPD)

2008-09-01 Thread Suman Chakrabarty
Dear all, since one of my mails with multiple questions went completely unanswered ( http://www.mail-archive.com/gmx-users@gromacs.org/msg15437.html ), let me try this time with more specific question. Is there any chance of Dissipative Particle Dynamics (DPD) being incorporated in Gromacs as a c