Dear gromas users, I am new to gromacs and trying to run polyacrylate MD simulation. I obtained an itp file using PRODRG (gromos 96 force-field parameters). When I compare with the same forcefield parameters in the gromacs/top directory, they are far too off. For eg.
[ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.125 13400000.0 0.125 13400000.0 ; CAC OAD 2 3 2 0.125 13400000.0 0.125 13400000.0 ; CAC OAE 4 2 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAC 4 5 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAA 4 6 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAG 7 6 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAG 7 8 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAI As I understand, the function type should be 1 and c1 values should correspond to the force constant for bond stretching. But here it corresponds to the pair wise non bond parameters as listed in the gromacs/top force-field file. Similarly, [ pairs ] ; ai aj fu c0, c1, ... 1 5 1 ; OAD CAA 1 6 1 ; OAD CAG 2 7 1 ; CAC CAH 3 5 1 ; OAE CAA 3 6 1 ; OAE CAG 4 8 1 ; CAB CAI 4 11 1 ; CAB CAL 5 7 1 ; CAA CAH there are no pair terms listed here in the pairs section. [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 126.0 770.0 126.0 770.0 ; OAD CAC OAE 1 2 4 2 117.0 635.0 117.0 635.0 ; OAD CAC CAB 3 2 4 2 117.0 635.0 117.0 635.0 ; OAE CAC CAB 2 4 5 2 109.5 520.0 109.5 520.0 ; CAC CAB CAA 2 4 6 2 109.5 520.0 109.5 520.0 ; CAC CAB CAG 5 4 6 2 109.5 520.0 109.5 520.0 ; CAA CAB CAG 4 6 7 2 109.5 520.0 109.5 520.0 ; CAB CAG CAH For angles also the fu term is 2 instead of 1, although the angle and the force constant parameters are correct. Similar errors are there in the dihedrals section also. This means I need to almost fully edit the itp file I got from PRODRG to proceed further. Thank you in advance for any help and please clarify whether the itp file from PRODRG is unreliable even while using GROMOS96 force field ? Thanking you, Dr. M. S Sulatha Women Scientist Chemical Engineering Dept. IIT-Madras, Chennai India
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