Re: User-defined forces in NAMD

From: Axel Kohlmeyer (
Date: Wed Apr 11 2012 - 13:32:26 CDT

On Wed, Apr 11, 2012 at 2:12 PM, Ali Ghaffaari <> 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.


> On Tue, Apr 10, 2012 at 9:25 PM, Ehsan Ban <> wrote:
>> Hi,
>> If you want to customize things I think it would be much easier to use
>> Bests
>> EHsan
>> On Tue, Apr 10, 2012 at 8:16 AM, Axel Kohlmeyer <>
>> wrote:
>>> On Apr 10, 2012, at 7:38 AM, Ali Ghaffaari <>
>>> 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
College of Science and Technology
Temple University, Philadelphia PA, USA.

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