I am trying to modify the original GROMOS 54a7 force field files implemented in GROMACS to add parameters of some new cations. But when I checked the ffnonbonded.itp, I found that the charge parameter of CU2+, Zn2+ equals to zero. Why? What does it mean? How GROMOS 54a7 force field calculate the electrostatic interaction? If I want to add some new ions, what should I do?
Thanks in advance.
Wojciech Kopec
Hi Wojciech,
Sorry to bother you again. I had another problem. When I tried to add parameters of Ni ion to ffnonbonded.itp. I found that there are three blocks: [ atomtypes ], [ nonbond_params ] and [ pairtypes ]. I want to know that what is the difference between [ nonbond_params ] and [ pairtypes ]. They all includes the C6, C12 of different atom pairs as shown below. From my observation, I found that [ nonbond_params ] doesn't include i-i pair. But why the C12 parameter of the same pair is different in these two blocks? What should I do if I want add Nickel ion info? Thank you very much.
[ nonbond_params ]
; i j func c6 c12
OM O 1 2.261954E-03 8.611000E-07
OA O 1 2.261954E-03 1.386510E-06
OA OM 1 2.261954E-03 2.258907E-06
OE O 1 2.261954E-03 1.100000E-06
OE OM 1 2.261954E-03 9.472100E-07
OE OA 1 2.261954E-03 1.505529E-06
[ pairtypes ]
; i j func c6 c12
O O 1 2.261954E-03 7.414932E-07
OM O 1 2.261954E-03 7.414932E-07
OM OM 1 2.261954E-03 7.414932E-07
OA O 1 2.261954E-03 9.687375E-07
OA OM 1 2.261954E-03 9.687375E-07
OA OA 1 2.261954E-03 1.265625E-06
Wojciech Kopec
For different atom types charges are mainly zero in the nonbonded file. The same can be compared with different force field files. When I generated topologies using ATB, I tried to match the charges only to find out the charges are zero there.- Badges
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