[gmx-users] gromacs impropers

alexander yakovenko yakovenko_a at ukr.net
Sun Jul 21 15:10:40 CEST 2002

Dear all,
Does anybody know about improper torsions in gromacs?
I have the system:
     |                        ||    
Its work well, while I don t add C4-C3-C2-C1  improper angle.
 From  semiempirical AM1 dynamic I know, that this angle is 0, but adding this information to gromacs topology reduce to wrong simulation (the correct simulation is AM1 dynamic). After  energy minimization the angle C4-C3-C2-C1 is more than 30 degrees.

The impropers topology of this molecule is:
[ impropers ]
 C4  C3  C2  C1  0.00   500.00
 C2  C3  C7  C1  0.00   500.00  
 C2  C3  C4  C5  0.00   500.00
 C3  C4  C5  C6  0.00   500.00
 C4  C5  C6  C7  0.00   500.00
 C5  C6  C7  C2  0.00   500.00
 C6  C7  C2  C3  0.00   500.00  
 C7  C2  C3  C4  0.00   500.00

Thank you.

Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
acad.Zabolotnogo str. 150
E-mail: yakovenko_a at ukr.net

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