AMBER Archive (2000)

Subject: Ewald parameters

From: Alexander Issanin (issanin_at_mail.uni-greifswald.de)
Date: Thu Mar 09 2000 - 06:26:40 CST


Dear Amber users!

I have a question about PME parameters specified in the end of sander
input (.mdin) file e.g. PME box parameters, size of charge grid and so
on. In AMBER 5 manual it is written that "this information must be
specified and _overrides_ the box information specified in the parm
file". On the other hand when I start NVT-dynamics after NPT, I can find
in output file something like:

----------------------------------------------------------
   EWALD SPECIFIC INPUT:

     Box X = 36.723 Box Y = 42.195 Box Z = 50.815
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 37 NFFT2 = 42 NFFT3 = 51
     Cutoff= 9.500 Tol =0.100E-04
     Interpolation order = 4
     Largest sphere to fit in unit cell has radius = 18.361
     Ewald Coefficient = 0.29051
-----------------------------------------------------------
(parameters from .mdin file)
and then

-----------------------------------------------------------
 Largest sphere to fit in unit cell has radius = 16.669
 NEW EWALD BOX PARAMETERS from inpcrd file:
     A = 34.82838 B = 33.33781 C = 45.31798

     ALPHA = 90.00000 BETA = 90.00000 GAMMA = 90.00000
-----------------------------------------------------------

My questions are:
1) Should I put new actual box parameters in .mdin file after
NPT-dynamics run (or they will be read automatically from .inpcrd file)?
2) How important are NFFT1..NFFT3 parameters for the accuracy of the
run? Is it better, when BOXX/NFFT > 1.0 or < 1.0?
3) What meaning has "Ewald error estimate" in the output file? What
value supposed to be appropriate?

 Thanks for the help!

Alex Issanin.