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