[gmx-users] Fwd: sigma unit conversion
Barnett, James W.
jbarnet4 at tulane.edu
Thu Mar 6 15:17:29 CET 2014
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:
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
I'm just someone who uses acpype occasionally, so I hope this is helpful.
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
> 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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