yes, this could be an issue. the format for the trajectory files is only set
to handle up to 100 million MD steps in a single run (between restarts).
Perhaps you did a really, really long single run of REMD that led to
overflow of this value.
you can change this bahavior in sander.f:
write (MDCRD_UNIT,'(a,3(1x,i8),1x,f8.3)') "REMD ", repnum,
mdloop, &
total_nstep, mytargettemp
let us know if that wasn't the case.
On Mon, Sep 13, 2010 at 7:35 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi,
>
> yes I have tried the temperature dependent trajectory which gives the same
> number of structures. I think I have found the error
>
> Checking coordinates: remd.mdcrd.001
> WARNING in checkCoordinates(), AMBER trajectory file is corrupted: '*'
> detected (remd.mdcrd.001)
>
> so when I look into the *mdcrd file
>
> REMD 1 200000 ******** 458.600
>
> * are introduced so it seems that it is skipping the rest of the
> coordinates
> after this?
>
> I have used VMD for the trajectory and I use the prmtop file - what tells
> me
> that there are to few trajectories is when I multiply the number in the
> mdin-file and I look at the number of structures written to the mdcrd-file
> which are the same number as I would expect from the my input parameter
> file.
>
> If I change f.ex
> REMD 1 200000 ******** 458.600
>
> to
> REMD 1 200000 9999999 458.600
>
> File (test.mdcrd.001) is an AMBER REMD (new format) trajectory, 1 files
> total (First index is 001), frames at 300.000000 K will be used, each file
> has 20000 sets
>
> the number of sets are increased where is earlier read
>
> File (remd.mdcrd.001) is an AMBER REMD (new format) trajectory, 12 files
> total (First index is 001), frames at 300.000000 K will be used, each file
> has 19999 sets
>
> So will probably need to change the ***** to a number?
>
>
>
>
>
> On Mon, Sep 13, 2010 at 1:13 PM, Adrian Roitberg <roitberg.qtp.ufl.edu
> >wrote:
>
> > Maybe you can try, just ONCE, to write the temperature trajectory from
> > the remd trajectory, and see if that mdcrd file behaves 'correctly' ?
> >
> > Adrian
> >
> >
> > On 9/13/10 1:09 PM, Carlos Simmerling wrote:
> > > 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
> > >>>> _______________________________________________
> > >>>> AMBER mailing list
> > >>>> AMBER.ambermd.org
> > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >> _______________________________________________
> > >> AMBER mailing list
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> > >>
> > > _______________________________________________
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> > >
> >
> > --
> > Dr. Adrian E. Roitberg
> > Associate Professor
> > Quantum Theory Project, Department of Chemistry
> >
> > Senior Editor. Journal of Physical Chemistry.
> >
> > on Sabbatical in Barcelona until August 2011.
> > Email roitberg.ufl.edu
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Sep 13 2010 - 06:00:06 PDT
