[gmx-users] nucleic acids simulation

Andrey V Golovin golovin at genebee.msu.su
Thu Jul 17 13:34:00 CEST 2003

Hello lpgomes,

lpfb> Iґve just finished a simulation (200ps) with crystallographic DNA dodecamer,
lpfb> and the results seem very good using OPLS and PME. Comparing to AMBER4.1 I 
lpfb> found better rmsdґs. H-bonds (between bases), in my case, were stable 
lpfb> through this time.
lpfb> But I donґt know how to help you. I have some questions too.
lpfb> Some of these problems with nucleic acid hbonds can be originated by 
lpfb> the "end effect", where the ends of molecules tend to move more and 
lpfb> consequently hbonds brake, but at the center residues we see stable hbonds.

Thanks for answer but ... there is no DNA/RNA residues in ffoplsaa.rtp

in gromacs 3.1.4 did you add it manually?

Best regards,
 Andrey                            mailto:golovin at genebee.msu.su

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