RE: [AMBER-Developers] [p.varnai.sussex.ac.uk: Re: [AMBER] Distance restraint and periodic boundary conditions]

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 21 Aug 2009 15:20:32 +0100

Hi All

> > (1) I think binary restart files (ntxo=0) are no longer allowed
> (amber10).
> > It would be good to re-enact this option though.
>
> I would second that. I tried running an MMPBSA nmode calculation
> yesterday
> and it breaks trying to use ntxo=0. Hacking the script to use ntxo=1 is
> a
> workaround, but results in a loss of precision, right? I dont know if
> many
> people use this way of entropy calculation ATM, but either the
> mmpbsa.pl
> script or the ntxo option need to be adjusted...

Is there a reason why we would want to go back to supporting binary restarts
rather than deciding on a way to write netcdf restarts? I think it would
make more sense to use netcdf no?

All the best
Ross


/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.





_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Aug 21 2009 - 08:11:08 PDT
Custom Search