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.
Received on Thu Mar 09 2000 - 04:26:40 PST
