On Fri, Apr 15, 2011, Ross Walker wrote:
[Moving this over to the amber-developers mailing list.]
>
> With regards to the second problem I think the issue here is that you end up
> with a bond that spans molecules.
Things like this impact imaging and the barostat. As for imaging, my
hope(?!?) is that people will move to a netcdf restart format, which should
greatly reduce the need to set iwrap=1 during dynamics. (Alternatively, the
iwrap code in sander/pmemd needs to become as sophisticated [and complicated]
as what is in ptraj.)
For the barostat:
In the short- to medium time frame (e.g. for Amber12) I think we should really
explore porting Dave Cerutti's(*) Monte Carlo barostat to pmemd. This avoids
calculation of the virial (and hence simplifies things by removing all the
code that relates to that) and doesn't require any knowledge of "molecules".
The cost is an extra energy evaluation at each step where a trial volume
change "move" is attempted. I *think* we will be able to do this only every
20-100 steps (especially for long simulations, where you would still get lots
of moves), which implies a 1-5% overhead, comparable to what we currently pay
for NPT vs NVT. Things like parallel scaling need to be addressed, but I
think that we can just use our current parallel technology for this.
(*) The original idea is not Dave's, but he has implemented this in mdgx, and
knows its ins and outs. See Section 11.3 of the version of the AmberTools
Users' Manual in the master branch.
...just some ideas....dac
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Received on Fri Apr 15 2011 - 11:00:02 PDT
