thx - yes over 100 million steps
On Mon, Sep 13, 2010 at 2:45 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > > >>>> _______________________________________________
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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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Received on Mon Sep 13 2010 - 07:30:03 PDT
