[gmx-users] ffamber94 parameters

Mark Abraham mark.abraham at anu.edu.au
Tue Oct 5 15:20:54 CEST 2010

As one of the early chapters in the GROMACS manual points out, GROMACS always uses energy and distance quantities in particular units. The use of kb depends on those conventions, so you should look up the relevant formulae for AMBER and GROMACS and see how the conversion should work (hint: there's a factor of 2 involved as well). Or, you could play around with 4.184J/cal and work it out in a minute or two :-)


----- Original Message -----
From: Artur Panczakiewicz <apanczakiewicz at gmail.com>
Date: Wednesday, October 6, 2010 0:14
Subject: [gmx-users] ffamber94 parameters
To: gmx-users at gromacs.org

> Dear All,
> Do you know what is the unit of kb in ffamber94bon.itp file? I 
> need to
> add some missing parameters for my system however I have them in
> kcal/mol and it seems that ffamber94 uses another units. For example:
>                             b0             kb
> C  O2         
> 1    0.12500   548940.8 ; 7,(1986),230; 
> GLU,ASP//taken from ffamber94bon.itp
> C  
> O2                 1.250        656,0 (kcal/mol)  //JCC, 7, 230, 1986
> Thank you in advcance for help!
> Regards,
> Artur
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