GROMACS version: 2019.3
GROMACS modification: No
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I’m using Slipids force field for the membrane with GAFF force field for the solute and I have converted what comes from antechamber with acpype in order to have a gromacs topology for the solute. I had some new atomtypes that I have put in a separate file from the force field main folder (slipids) with the topology file being like this:
My question is does gromacs appends both files with the atom-types (one from the slipids and the other one with the new-atomtypes.itp file)?. If Gromacs needs to override a particular parameter which one will it take? The one from the last file?
The last question is concerning the way the atomtypes are written in the files. In the slipids force field they are written like this:
[ atomtypes ]
;name at.num mass charge ptype sigma epsilon
HAL1 1 1.008000 0.09 A 0.235197261589 0.092048
And in the “new-atomtypes.itp” file they are written in the same way as OPLS force field, like this:
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
h1 h1 0.00000 0.00000 A 2.47135e-01 6.56888e-02
Is this a problem? Does GROMACS know what are the sigma and epsilon in booth situation? I have tested and it doesn’t seem to be a problem, but how does GROMACS recognize the differences?
Thank you in advance.