Hi Maria,
On Jul 30, 2012, at 5:16 PM, Maria Minakova <mariabiophysics.gmail.com> wrote:
> Thank you all for your replies and suggestions!
> I ended up adding a small non zero vdw radius. The minimization went alright, so did heating and initial equilibration, no collapse or significant structure distortion observed.
> I experience some problems with npt equilibration, but right now I have no reason to connect them with (ho) atom type behavior (...-PO3H2).
>
> This (ho) atom type problem has been discussed in the community before,
> so I attached a few links in case somebody finds them useful.
>
> http://code.google.com/p/acpype/wiki/FAQ
> http://structbio.vanderbilt.edu/archives/amber-archive/2003/1967.php
> http://archive.ambermd.org/200607/0109.html
> Matthew Terrier suggested to modify (ho) vdw params in here:
> http://archive.ambermd.org/201110/0119.html
> I could not find the actual publication behind this modification, it could be a conference poster or an oral presentation.
I think it's more of a "this addition has little to no impact on results, but prevents catastrophic collapses.
Actually, pmemd.cuda automatically applies a value of 0.5 angstroms as the sigma value (or epsilon? I always get those confused) for atoms whose vdw parameters are 0 and we've seen no ill effects so far (and the code gets tested pretty thoroughly).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 30 2012 - 15:30:02 PDT
