AMBER Archive (2004)

Subject: RE: AMBER: MD & running time

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Wed Jun 23 2004 - 14:53:13 CDT

I was under the impression that the information Ross Walker gave (below) about
ntx=5 and ntx=7 in Amber 8 was also true for Amber 7--basically that they do
the same thing and ntx=7 was there for backwards compatibility--but not for
Amber 6, where they have different definitions. If this is not true, then I am
in big trouble...
 
Kristina

>===== Original Message From "Ross Walker" <ross_at_rosswalker.co.uk> =====
>> > 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
>

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu

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