Re: [gmx-users] FENE potential (Finitely extensible Nonlinear elastic model)

2008-08-29 Thread David van der Spoel
avinash kumar wrote: Dear All, Can FENE be implemented in GROMACS code? The description of FENE is: FENE is primarily for the bead-spring-type polymer model. It is a bonded interaction. Explicitly, its standard form is: E = -0.5 K R0^2 * ln[1 - (r/R0)^2] r = distance (btw two con

[gmx-users] FENE potential (Finitely extensible Nonlinear elastic model)

2008-08-29 Thread avinash kumar
Dear All, Can FENE be implemented in GROMACS code? The description of FENE is: FENE is primarily for the bead-spring-type polymer model. It is a bonded interaction. Explicitly, its standard form is: E = -0.5 K R0^2 * ln[1 - (r/R0)^2] r = distance (btw two connected beads) coeff1

Re: [gmx-users] FENE potential

2006-12-13 Thread Tsjerk Wassenaar
Argyrios, I do consider my reply right on the spot, since it showed that, in the most current version of gromacs and the documentation thereof, there was indeed a FENE bond type. If no additional information is given, and none was given, we will assume that the query applies to the latest version

Re: [gmx-users] FENE potential

2006-12-11 Thread Mark Abraham
> First of all in the gromacs manual 3.2, that i have on page 51 there is > the LJ and Buckingham potential and in chapter 4.2.4 (page 58) the > harmonic potential is discussed, so page 51 and chapter 4.2.4 talk about > different things. That would be why it would be good for you to be looking in

[gmx-users] FENE potential

2006-12-11 Thread Argyrios Karatrantos
Hi, More than possible, it has already been done. Manual chapter 4.2.4, page 51. And please give me a very good reason why I now picked up the manual and looked for FENE, instead of you. My bad... :-P I assumed someone would read the available documentation resources before posting on this lis

Re: [gmx-users] FENE potential-bond interaction

2006-12-11 Thread Mark Abraham
> Hi, > > More than possible, it has already been done. Manual chapter 4.2.4, > page 51. And please give me a very good reason why I now picked up the > manual and looked for FENE, instead of you. My bad... :-P I assumed someone would read the available documentation resources before posting on th

Re: [gmx-users] FENE potential-bond interaction

2006-12-11 Thread Tsjerk Wassenaar
Hi, More than possible, it has already been done. Manual chapter 4.2.4, page 51. And please give me a very good reason why I now picked up the manual and looked for FENE, instead of you. Tsjerk On 12/11/06, Mark Abraham <[EMAIL PROTECTED]> wrote: Argyrios Karatrantos wrote: > HI, > is it possi