AMBER Archive (2004)

Subject: Re: AMBER: Box of mixed solvant

From: Dr. Yong Duan (yduan_at_albert.chem.udel.edu)
Date: Wed Feb 11 2004 - 00:09:28 CST

My (wild) guess is that the box was not set in leap when you
constructed the system. IFBOX only comes from prmtop, as you noted and it
is set in leap. You can set the box in leap (setbox).
Sander allows you to do simulation with NTB.ne.0 and IFBOX.eq.0. (should
this be changed?)
"totally blown up" is not necessarily a bad thing at all (no kidding).
This is typically related to imaging operations. So long as your density
remains reasonable, the system should be ok. In your case, it might be an
indication of problem (because IFBOX=0). Check the energy output. If you
find a line telling you about the density and it is not too low, you are
ok. If you can not find the line or if your density is too low, you
probably need to reconstruct the system or re-run the equilibration.

Good luck!

yong
On Wed, 11 Feb 2004, FyD wrote:

> Dear Amber user,
>
> I try to build a box of solvent composed of 2 different solvants (different percentages). Using
> leap, I got prmtop & prmcrd files of a box of solvent composed of 2 different solvants. My
> equilibration protocole is the following: - (i) Minimization, (ii) a MD from 100-300 K (cst vol.) and
> (iii) finally a MD at 300 K (cst pres.). I have 2 questions:
>
> -1- After step (ii), I checked the box shape : it has totally blowed up. Does it make sense ?
>
> -2- Step (iii) stopped with the following error message: "(NTB.ne.0 && NTP.ne.0) but
> IFBOX.eq.0 This combination is not supported". I checked the anwer by Bill Ross @0146.html
> "IFBOX comes from the prmtop, 0 indicates that there is no box for the model - and the other
> options indicate that a box is needed." As the prmtop file is the same in the three steps, I do
> not understand why I get this message only for the 3rd step...
>
> Thank you very much, best regards, Francois
>
>
>
>
>
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