MD with 'Solvated Ions'

From: Andreas Svrcek-Seiler <>
Date: Mon 15 Jan 2001 15:19:30 +0100 (CET)

Has anyone out there done 'successful' Vacuum MD with
nucleic acids and the 'IB' ions ? My attempts led to distorted structures
despite VERY long equilibration holding the 'solute' fixed and doing
Brownian dynamics at 300K with the positive ions using many large
Of course the nucleic acid structure was a 'good one', i.e. it was a
RNA-tetraloop that was also used as starting point for a stable
multi-nanosecond implicit solvent (GB/SA) MD run using underdamped
Langevin dynamics. So, am i doing something wrong or trying something
that can not work at all ?

Thanks in advance
W. A. Svrcek-Seiler

           ( O O )
              o Wolfgang Andreas Svrcek-Seiler
              o (godzilla)
      .oooO Tel.:01-4277-52733
      ( ) Oooo.
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Received on Mon Jan 15 2001 - 06:19:30 PST
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