[gmx-users] errors in ffG43a2nb.itp

[Marcos Villarreal]

Hello ,

I have noticed some errors in ffG43a2nb.itp as well as in ffG43a1nb.itp and
ffG43b1nb.itp
The most obvious is that  while atom type NR have a bigger c12 param than the
others Nx atoms, the [ nonbond_params ] lines are the same
e.g.
       C       NT  1  0.0023880368  2.389937e-06
       C       NL  1  0.0023880368  2.389937e-06
       C       NR  1  0.0023880368  2.389937e-06

     CH2       NT  1  0.0041605544  6.605177e-06
     CH2       NL  1  0.0041605544  6.605177e-06
     CH2       NR  1  0.0041605544  6.605177e-06

The are some other errors. Like:
the line
       C       OW  1  0.0024751208  2.836328e-06
should be
       C       OW  1  0.0024751208  2.981451e-06

All the errors seems to be in the c12 param.


How the param for [ pairtypes ]  are calculated?

Saludos,


PD: If it is of any help, I wrote this simple tcl script to calculate the
combined param

#!/usr/bin/tclsh

set I6   0.0023406244  ;#c6  for C type
set I12  3.374569e-6   ;#c12 for C type

set filer [open vdw.dat r]    ;#the head of ffG... without the first two lines
set filew [open vdw.out w]

while {[gets $filer linea] >= 0} {

    set t   [lindex $linea 0]
    set J6  [lindex $linea 4]
    set J12 [lindex $linea 5]

    set a [expr sqrt($I6  * $J6 )]
    set b [expr sqrt($I12 * $J12)]

    puts $filew "       C       $t  1  $a  $b"
 }
--
Marcos Villarreal
Grupo de Biofisica
Departamento de Quimica Biologica - CIQUIBIC.
Universidad Nacional de Cordoba.
Corodba. Argentina.