AMBER Archive (1999)

Subject: Re: PME question

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Thu Dec 16 1999 - 17:09:27 CST

Dear francesca,
I'm not sure but I imagine BOXX etc. might be from the bottom of the parm
file. Often these are large at beginning, giving low density.
If so they are ignored by PME and the values you input are used (at least
the code in amber4.1 and amber5.0 is supposed to work that way.)
hope this helps
Tom D

On Thu, 16 Dec 1999 francy_at_mvcch3.unica.it wrote:

> Hi,
>
> I have a question about PME.
>
> in sander input I set BOXX, BOXY etc. as follow (the BOX values taken
> from the restart file):
>
> (....)
> iewald = 1,
>
> &end
> 46.4018127 46.2963706 57.3089329 90.0000000 90.0000000 90.0000000
> 45 45 60 4 0 0 0
> 0.00001
>
> in sander output I find:
>
> (.....)
> 1. RESOURCE USE:
>
> EWALD SPECIFIC INPUT:
>
> Box X = 46.402 Box Y = 46.296 Box Z = 57.309
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 45 NFFT2 = 45 NFFT3 = 60
> Cutoff= 9.000 Tol =0.100E-04
>
> (...)
>
>
> 2. CONTROL DATA FOR THE RUN
>
> (...)
>
> NTB = 2 IFTRES= 1 BOXX = 51.261
> BOXY = 51.145 BOXZ = 63.496
>
> (....)
>
> My question is: where do the last values of BOXX, BOXY and BOXZ come from?
>
> thanks in advance,
>
> francesca
>