it's not possible to help unless you specify which version of sander and
which version of ptraj/ambertools.
On Mon, Sep 13, 2010 at 6:19 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi all,
>
> I have performed a remd with a 250.000 number of exchange trials during the
> simulation every 0.5 ps. I have set ntwx=5.000 so I would expect 25.000
> structures in my simulation but after processing the data using the script
> to extract the coordinates at different temperatures I get
>
> #!/bin/csh
>
> ptraj l_dermorphin.prmtop << EOF
> trajin remd.mdcrd.001 remdtraj remdtrajtemp 300.0
> trajout remd.300K.mdcrd nobox
>
> distance d1 out dist.300K.dat :1.CA :7.CA
>
> go
> EOF
> which reads all the output files
>
> Processing AMBER REMD trajectory (new format) files remd.mdcrd.001 ->
> remd.mdcrd.010
>
> I only get 19999 structures - when I grep *REMD*' in the mdcrd.001 file I
> get 25.000 lines with REMD as expected. I do not know where my mistake is
> any help appreciated
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Received on Mon Sep 13 2010 - 04:00:03 PDT
