Dear all Gmxers,I am calculating a mutation free energy from L<->A for a five AA peptides using G96 53a6 force field.
however, my dG_for and dG_rev is quite different. dG_for(lambda=0.00) = - 9.9 kJ/mol dG_rev(lambda=1.00) = 1.33 kJ/mol
Is there anything wrong with setting up topologies?Here is the [atoms] part for morphed atoms. and I attached the full .top in the attachment.
For L->A: [ atoms ]17 CH2 2 LEU CB 6 0 14.027 CH3 0 15.035; qtot 1 18 CH1 2 LEU CG 7 0 13.019 DUM 0 13.019; qtot 1 19 CH3 2 LEU CD1 7 0 15.035 DUM 0 15.035; qtot 1 20 CH3 2 LEU CD2 7 0 15.035 DUM 0 15.035; qtot 1
For A->L : [ atoms ]17 CH3 2 ALA CB 6 0 15.035 CH2 0 14.027; qtot 1 60 DUM 6 DUM DUM 24 0 13.019 CH1 0 13.019 61 DUM 6 DUM DUM 24 0 15.035 CH3 0 15.035 62 DUM 6 DUM DUM 24 0 15.035 CH3 0 15.035
thanks for help LQ
topol_A2L.top
Description: application/extension-top
topol_L2A.top
Description: application/extension-top
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