[gmx-users] Fwd: sigma unit conversion

[Barnett, James W.]

The Amber molecular dynamics program (sander) uses a different format of the 
van der Waals equation, so Amber force fields are designed to use different 
parameters than those used in Gromacs. So, it's not as simple as converting 
from Angstroms to nanometers. The coefficents used in the Amber force fields 
are not simply Gromacs sigma and epsilon.

Here is a document related to your question from the Amber site:
http://ambermd.org/Questions/vdwequation.pdf

Additionally combination rule 2 in Gromacs is a Lorentz-Berthelot rule (see 
section 5.3.2 in the Gromacs manual). This is just how the force field was 
designed. 

I'm just someone who uses acpype occasionally, so I hope this is helpful.

James Barnett

On Wed, Mar 05, 2014 at 10:17:27PM -0600, Chetan Mahajan wrote:
> 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
>      Amb
>  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 ?)
> 
> Thanks
> Chetan