From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Tue Jun 26 2007 - 10:27:25 CDT
Hi all,
I should clarify NNB (non-bonded interaction ) section when I create psf with
alchemify program.
In the NNB section of new psf file are present only atoms with lambda values
of 1 in file.fep .
Why not there are atoms with lambda equal to -1 ?
These atoms do not interact each other but in NNB section they are only of
one type.
It is wrong?
Which is the format of NNB in PSF file?
example:
PDB or Fep file:
ATOM 19 HB2A STA 2 40.764 46.498 10.639 1.00 -1.00
ATOM 20 OGA STA 2 42.181 47.086 9.211 1.00 -1.00
ATOM 21 HG1A STA 2 42.884 46.570 8.738 1.00 -1.00
ATOM 22 CBB STA 2 41.325 46.085 9.771 1.00 1.00
ATOM 23 HB1B STA 2 41.965 45.250 10.138 1.00 1.00
ATOM 24 HB2B STA 2 40.764 46.498 10.639 1.00 1.00
ATOM 25 ..
ATOM 26..
PSF file:
30 !NNB
22 23 24 25 26 27 22 23
24 25 26 27 22 23 24 25
26 27 22 23 24 25 26 27
22 23 24 25 26 27
Thanks in advance
Luca
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