[gmx-users] sigma unit conversion

Chetan Mahajan chetanvm10 at gmail.com
Thu Mar 6 05:14:47 CET 2014

Hi all,

I am using Amber2gromacs tool called as acpype for converting input files
to Amber to input files for gromacs. I have a question regarding atomtypes
section of .top file. Here are first two rows of that section in my file:

name   bond_type     mass     charge   ptype   sigma         epsilon
 Ti           Ti            0.00000  0.00000    A     1.39461e-01
6.08772e-02 ; 0.78  0.0145
 OT       OT            0.00000  0.00000    A     2.87832e-01   8.29687e-02
; 1.62  0.0198

Now, in my .top file, each row contains, at the end, Amber force field
values for sigma and epsilon are given. Values on the left indicate unit
converted values. However, given that Amber units are A0 for sigma,
converted value for gromacs, which should be in nanometer does not match.
Combination rule chosen is 2. ( by the way, how is this rule chosen ?)


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