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Hello, Ross and Bill:
Thank you very much for the advice. I use Amber7 for the MD run. Amber 8
is not available yet under the local access. Thanks to remind me the
difference between the two visions. I will give a try with 'ntx=7' and
see how is going.
Best regards
Bo Yang
On Tue, 22 Jun 2004 20:51:28 -0700 "Ross Walker" wrote:
>
>
> > > After the run, I notice that there are significant changes
> > on the protein
> > > structure, especially at the helix regions. Most helixes
> > are disordered
> > > and turn into loops.
> >
> > With ntx=5 the pressure/density-equilibrated box was restored to
> > the size of your initial model (7 is the correct value). Thus your
> > system was subjected to a sudden vacuum, which may explain the
> > disordering.
> >
>
> This is no longer true in Amber 8. In Amber 8 NTX=7 is the same as
> NTX=5 and
> is included for backwards compatibility.
>
> Note: The definition of NTX=5 is now:
>
> "X and V are read formatted; box information will be read if ntb>0.
> The velocity information will only be used if irest=1."
>
> Hence if ntb>0 then NTX=5 is equivalent to the old definition of
> NTX=7. I.e
> the current box size is read from the inpcrd file.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
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Received on Wed Jun 23 2004 - 05:53:00 PDT
