AMBER Archive (2005)

Subject: Re: AMBER: spherical boundary condition

From: Hui-Hsu Tsai (tsaih_at_ncifcrf.gov)
Date: Mon Mar 14 2005 - 12:59:01 CST

Andreas,

Thanks for your valuable comment.

Yes, what you say below is exactly what I want.

The basic requirements of my simulation are to keep concentration
of system constant and also enhance the collision rate betwee peptides.
Based on these two requirement I think using the spherical boundaty condition
seems a good solution.

It's fun to modify code, however, debugging and testing is time consuming.
Before changing the codes, I am still seeking for an alternate, but simple
solution. I try to use periodic boundary condition in GB simulation.
Unfortunately, Amber GB is not compatible with PBC.

I am thinking to weakly restrain all peptides to origin points...
I am a new amber user, any comment is welcomed.

Thanks.

Gavin

On Mon, 14 Mar 2005, Andreas Svrcek-Seiler wrote:

>
> Hi,
> If you restrain multiple peptides by an elastic spherical wall
> outside, they might go ballistic insite the cavity, sometimes
> bouncing off the wall or off each other. Are you sure you want that?
> *If* you really want that, you could change the code for the harmonic
> restraints (sorry - I don't know where that is in the AMBER code).
> Then, setting all restraint positions (e.g.) to zero,
> you'd just have to change the restraint potential to whatever you want if
> |r - r0| > R_restraint , zero otherwise (and never forget to fix the
> gradient).
> If you want that and don't want/dare to fiddle with the fortran code,
> you could try NAB
> (http://www.scripps.edu/mb/case/casegr-sh-3.2.html)
> instead. In this case I could simply send you the patch
> and explain how to use it.
>
> Generally, if you explain what you want to do in more detail,
> more people might be able to help you.
>
> regards
> Andreas
>
>
>

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