Re: MD with 'Solvated Ions'

From: Bill Ross <>
Date: Mon 15 Jan 2001 11:19:15 -0800 (PST)

        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

I'm not clear on the protocol here - sounds like a non-amber

        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 ?
Nucleic acids in my experience do not hold up to 300K plain vacuum
dynamics, with or without ions, and probably even in quadruplex
form. If I had to run plain vacuum, I'd run a lower temperature or beef
up the base-base hbonds with restraints. Either way, the results are
compromised, but this is already the case with plain vacuum.

I haven't tried GB/SA etc.

Bill Ross
Received on Mon Jan 15 2001 - 11:19:15 PST
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