The KBFF or Smith urea model is widely recommended for simulations. It has some particular parameters as outlined in the paper attached and it follows the geometric combination rule. In an earlier question in this forum, I'd asked how KBFF model of urea could be incorporated in force fields that employ LOrentz Berthelot combination rule. I had got the answer that unless those specific combination rules are followed as in the original reference , we cant really term it as that particular solute model.
The OPLS ff, follows an all geometric combination rule and hence I have chosen it for modelling the KBFF urea model in the GROMACS package. To distinguish the Smith model parameters, I introduced new atomtypes with the specific non-bonded parameters with entry in the ffnonbonded.itp as :
;additional adding:Smith model
opls_966 CS 6 12.01100 0.921 A 3.77000e-01 4.17000e-01
opls_967 NS 7 14.00670 -0.693 A 3.11000e-01 5.00000e-01
opls_968 OS 8 15.99940 -0.675 A 3.10000e-01 5.60000e-01
opls_969 HS 1 1.00800 0.285 A 1.58000e-01 0.88000e-01
Later I have specified other bonded parameters and charges in a separate itp file. (trial1.itp is attached).
The minimization is very difficult to converge (more than 10000 steps in steepest descent). I have some confusion whether the bonded parameters that I have used in the itp file have been correctly assigned the proper units or not. For instance, the GROMOS96 parameters have been applied for bonds. The rest have been taken form the paper.
Could anyone who's working with these specific solute model please advise me as to how to proceed correctly? Any sample itp file will also be welcome.
Hi Apramita,
A series of about 150 different equilibrated liquids validated for use with GROMACS, and for the OPLS/AA and GAFF force fields, can be found at virtualchemistry.
http://virtualchemistry.org/
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