Re: User-defined forces in NAMD

From: Ali Ghaffaari (ali.ghaffaari_at_gmail.com)
Date: Wed Apr 11 2012 - 13:51:51 CDT

I've got your point, now! It's a valuable guide. I'll do what you said.

Thanks a lot!

On Wed, Apr 11, 2012 at 11:02 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Apr 11, 2012 at 2:12 PM, Ali Ghaffaari <ali.ghaffaari_at_gmail.com>
> wrote:
>
> > Dear Axel,
> >
> > The problem is clear for me. But I don't want to implement a simulator
> from
>
> nobody said that you should do that. although,
> implementing a small MD code for LJ particles
> only is about the fastest and best method to
> learn the MD basics. it will be much easier
> afterwards to work with an already written
> code that has many more features.
>
> > scratch! Besides, I've just started to study MD and I need time to be
> > experienced. Thanks for your advice!
>
> but that is exactly what i am saying.
>
> before you can start modifying you
> should *first* learn how to use an
> MD code correctly. if you first implement
> your custom interactions, then you'll
> never be able to tell whether a problem
> is due to your limited MD experience
> or a bug in your code, and in some
> cases you may not even be able to
> tell if there is a problem or not.
>
> axel.
>
>
>
> > On Tue, Apr 10, 2012 at 9:25 PM, Ehsan Ban <ehsan.ban_at_gmail.com> wrote:
> >>
> >> Hi,
> >>
> >> If you want to customize things I think it would be much easier to use
> >> LAMMPS.
> >>
> >> Bests
> >> EHsan
> >>
> >>
> >> On Tue, Apr 10, 2012 at 8:16 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> >> wrote:
> >>>
> >>>
> >>>
> >>> On Apr 10, 2012, at 7:38 AM, Ali Ghaffaari <ali.ghaffaari_at_gmail.com>
> >>> wrote:
> >>>
> >>> > Hello,
> >>> >
> >>> > I'm not skilled in MD. I have question about force field using NAMD.
> As
> >>> > I read in a NAMD documentation, it's using five potential energies:
> U(bond),
> >>> > U(angle), U(dihedral), U(vdW), and U(Coulomb). I want to simulate a
> protein
> >>> > by using a custom potential function for each atom rather than these
> five
> >>> > potential energies. How can I do that? Is it possible by using NAMD?
> or
> >>> > other MD tools?
> >>>
> >>> To be able to properly do that you *first* have to become experienced
> in
> >>> MD. It is not a matter of the tool, but a matter of understanding.
> Starting
> >>> a project you don't understand is a recipe for disaster.
> >>>
> >>> Axel
> >>>
> >>>
> >>>
> >>>
> >>> >
> >>> > Thanks a lot,
> >>> > Ali
> >>>
> >>
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>

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