AMBER Archive (2008)

Subject: RE: AMBER: igb and ibelly

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 30 2008 - 15:16:11 CDT

Hi Holly,

The code to do it is missing. GB calculations use a completely different
code branch in sander than do PME or vacuum calculations. I think you can
use belly with GB as long as you only fix the last atoms. I.e. a continuous
set of atoms that includes the last one (or perhaps it is the first) I
forget. I did fix the code at some point to allow ibelly to be used with GB
for an arbitrary set of atoms. I think it was against some version of AMBER
9 but I don't recall if it was the released version or a specific
development version.

Anyway, you can try the attached patch against amber 9 and see what happens.
Beware that the reason this never made it into the main code tree was
because I didn't have the time to actually check that it was correct, gave
the correct answer etc. So caveat emptor...

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Holly Freedman
> Sent: Friday, May 30, 2008 12:23 PM
> To: amber_at_scripps.edu
> Subject: AMBER: igb and ibelly
>
> Dear AMBER help,
> Can someone please explain to me why it is that the ibelly option is not
> allowed with igb>0
> (Generalized Born)? I don't understand how the two options are connected.
> Holly
>
> --
> Department of Physics, University of Alberta
> Edmonton CANADA
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu