> > 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
