AMBER Archive (2006)

Subject: Re: AMBER: How to specify user defined force fields or its parameters in amber??

From: Gobind Singh Bisht (gsbisht1_at_gmail.com)
Date: Tue Nov 28 2006 - 08:34:36 CST

Hi carlos,
              isn't it possible that u make Kr=0 for all the bonds or few
bonds in my system. That way i indirectly drop the bond term wherever i need
without doing programming??
              although i know programming, I need to know where all i need
to make the changes. How do i get those details?
thanx for ur cooperation

On 11/28/06, Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
>
> no, you cannot easily change the functional form without doing
> programming.
> I was referring to your question about using your own set of parameters.
> We do provide source code for people that are capable of changing
> the functional form of the energy equation.
>
> Gobind Singh Bisht wrote:
>
> > Hi carlos,
> > I could not find any directions to change the energy eqn of
> > the Classical amber force field i.e drop some terms or add some new
> > terms with their parameters. how shld i do that?
> >
> > On 11/28/06, *Carlos Simmerling* <carlos_at_csb.sunysb.edu
> > <mailto:carlos_at_csb.sunysb.edu>> wrote:
> >
> > yes, it is possible and quite common to modify parameters.
> > I suggest that you work through some of the Amber tutorials
> > that show how to do this. Check the Amber page or Ross Walker's
> > page:
> > http://www.rosswalker.co.uk/tutorials/amber_workshop/
> >
> > then you can ask questions about things that are not covered in
> > any of the tutorials.
> >
> > Gobind Singh Bisht wrote:
> >
> > > Dear amber users,
> > > Is thr anyway you can specify a user
> > > defined force field in amber or atleast your own set of
> parameters?.
> > > One way could be change edit the source code itself or the
> parameter
> > > files. Even if u have to do that, U need to know the structure
> > of the
> > > source code, which i dont. Can someone help me or guide me to some
> > > tutorial.
> > > thanx in advance
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu