Amber11 is the latest for sander.
so in the ptraj output it says that there are 20,000 frames, and has a dot
for each? it reads all without error?
and you are using the same prmtop to read the output trajectory? is it
correct? meaning have you visualized the output trajectory using something
like VMD, and the frames are correct but there are too few? what it is that
tells you there are too few frames?
thanks, these will help troubleshoot your problem.
On Mon, Sep 13, 2010 at 7:04 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> sure - I am using amber10 and ambertools 1.4 which should be the lastest.
>
> On Mon, Sep 13, 2010 at 12:41 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > 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 - 04:30:05 PDT
