Awesome, thanks Dan!
So the compiling went smooth with those modifications, as did the make
install. And when I ran the diffusion calculation on the it appears as
though the jumping msd issue is fixed even without having to unwrap the
trajectory! I did have to modify the diffusion command in the ptraj script
from averaging over the 2ps between each frame:
diffusion :DEF average diffDEF.out 2
to more simply:
diffusion :DEF diffDEF.out
But it seems like it worked and I kinda like how it outputs the diffusion
slope and fit coefficient in the ptraj.out file! Thanks
On Wed, Mar 9, 2016 at 12:54 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> The GitHub cpptraj is a standalone install and should be done in its
> own directory.
>
> Anyway, since you have amber 14 the sander API there is probably not
> compatible with the current iteration of cpptraj anyway. So disable
> that as well:
>
> ./configure -amberlib -nobzlib -nosanderlib gnu
>
> -Dan
>
> On Wed, Mar 9, 2016 at 12:24 PM, Timothy Christopher Schutt
> <tschutt.mymail.mines.edu> wrote:
> > I don't think it installed - what I sent was the entirety of the prompt
> it
> > gave me. I tried to type make install to test if it had configured and
> it
> > said it couldn't without a config.h file so my guess is that the
> configure
> > didn't finish without the sander API thing.
> >
> > Does this need to be performed in the ambertools bin folder? I've been
> > trying to do it in a separate directory so as to preserve the working
> > cpptraj just in case... My thought was that it could find all the
> necessary
> > files even from a remote directory since amberhome is set but am I wrong
> in
> > that perhaps?
> >
> > On Wed, Mar 9, 2016 at 11:07 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> In other words you should still see:
> >>
> >> CPPTRAJ configuration complete.
> >>
> >> On Wed, Mar 9, 2016 at 11:06 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> > Does configure actually fail at that point? It should just disable
> >> > linking to the sander API.
> >> >
> >> > On Wed, Mar 9, 2016 at 11:02 AM, Timothy Christopher Schutt
> >> > <tschutt.mymail.mines.edu> wrote:
> >> >> ./configure -amberlib -nobzlib gnu
> >> >>
> >> >> Assuming 64 bit architecture.
> >> >> Using BLAS/LAPACK/ARPACK/NetCDF libraries in
> >> /home/mtux7/Software/amber14
> >> >> Not using bzip2
> >> >> SANDER API will be used if found.
> >> >> Using gnu compilers
> >> >> Installing cpptraj binary to
> >> >> /home/mtux7/Software/Betacpptraj/cpptraj-master/bin
> >> >>
> >> >> Testing C compiler:
> >> >> OK
> >> >> Testing C++ compiler:
> >> >> OK
> >> >> Testing Fortran compiler:
> >> >> OK
> >> >> Checking ZLIB
> >> >> OK
> >> >> Checking NetCDF
> >> >> OK
> >> >> Checking LAPACK/BLAS
> >> >> OK
> >> >> Checking ARPACK
> >> >> OK
> >> >> Checking availability of the SANDER API from AmberTools
> >> >> Using SANDER API from /home/mtux7/Software/amber14
> >> >> ./testp: error while loading shared libraries: libsander.so: cannot
> open
> >> >> shared object file: No such file or directory
> >> >> Warning: Compilation with the SANDER API failed. Error follows:
> >> >> --------------------
> >> >> --------------------
> >> >>
> >> >>
> >> >> On Wed, Mar 9, 2016 at 8:41 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> >>
> >> >>> Hi,
> >> >>>
> >> >>> Admittedly the configure process could (and should) be made a bit
> >> >>> easier. By default cpptraj assumes you want certain libraries for
> full
> >> >>> functionality. In this case, bzlib is for reading bzip2-compressed
> >> >>> files (i.e. those with a .bz2 extension). The Amber configure script
> >> >>> automatically disables this when bzlib is not available. You can
> >> >>> either install the bzip2 development headers/libraries via your
> >> >>> package manager (I think it's usually called libbz2-dev or
> >> >>> bzip2-devel) or you can disable bzip2 support with '-nobzlib'.
> Typing
> >> >>> ./configure --full-help will give you a full list of configure
> >> >>> options.
> >> >>>
> >> >>> So try ./configure -amberlib -nobzlib gnu and see if that works.
> >> >>>
> >> >>> -Dan
> >> >>>
> >> >>>
> >> >>> On Tue, Mar 8, 2016 at 11:43 PM, Timothy Christopher Schutt
> >> >>> <tschutt.mymail.mines.edu> wrote:
> >> >>> > I apologize for my slow reply - I did try that at first but it
> came
> >> up
> >> >>> with
> >> >>> > a BZLIB error. $AMBERHOME is set in the ~/.bashrc and the .bashrc
> is
> >> >>> > sourced. This is what it gave me? I was lost so I went home and
> ate
> >> some
> >> >>> > dinner first.
> >> >>> >
> >> >>> > xxxxx$ ./configure -amberlib gnu
> >> >>> >
> >> >>> > Assuming 64 bit architecture.
> >> >>> > Using BLAS/LAPACK/ARPACK/NetCDF libraries in
> >> /home/mtux7/Software/amber14
> >> >>> > SANDER API will be used if found.
> >> >>> > Using gnu compilers
> >> >>> > Installing cpptraj binary to
> >> >>> > /home/mtux7/Software/Betacpptraj/cpptraj-master/bin
> >> >>> >
> >> >>> > Testing C compiler:
> >> >>> > OK
> >> >>> > Testing C++ compiler:
> >> >>> > OK
> >> >>> > Testing Fortran compiler:
> >> >>> > OK
> >> >>> > Checking BZLIB
> >> >>> > ./configure: line 131: ./testp: No such file or directory
> >> >>> > Error: Unable to compile using:
> >> >>> > g++ -I/home/mtux7/Software/amber14/include -o testp
> >> testp.cpp
> >> >>> > -lbz2
> >> >>> > Please check your compiler settings or configure flags. Error
> >> follows:
> >> >>> > --------------------
> >> >>> > testp.cpp:2:19: fatal error: bzlib.h: No such file or directory
> >> >>> > #include "bzlib.h"
> >> >>> > ^
> >> >>> > compilation terminated.
> >> >>> > --------------------
> >> >>> >
> >> >>> > Thanks for all the help, all of you!!
> >> >>> >
> >> >>> > On Tue, Mar 8, 2016 at 9:43 PM, Daniel Roe <
> daniel.r.roe.gmail.com>
> >> >>> wrote:
> >> >>> >
> >> >>> >> On Tue, Mar 8, 2016 at 6:05 PM, Timothy Christopher Schutt
> >> >>> >> <tschutt.mymail.mines.edu> wrote:
> >> >>> >> >
> >> >>> >> > .Daniel: I'm having trouble compiling the beta cpptraj - I'm
> >> pretty
> >> >>> new
> >> >>> >> to
> >> >>> >> > linux and command line stuff so I'm sure that part is just me
> >> being
> >> >>> slow
> >> >>> >> > but I'll figure it out here eventually.
> >> >>> >>
> >> >>> >> If you give some more specifics about what is going wrong I may
> be
> >> >>> >> able to help. With the latest GitHub version of cpptraj with
> Amber
> >> >>> >> already installed and AMBERHOME correctly set it should be as
> simple
> >> >>> >> as:
> >> >>> >>
> >> >>> >> ./configure -amberlib gnu
> >> >>> >>
> >> >>> >> (Assuming of course you are using gnu compilers). Let me know if
> you
> >> >>> >> need any more help,
> >> >>> >>
> >> >>> >> -Dan
> >> >>> >>
> >> >>> >> >
> >> >>> >> > .Thomas: I just attempted the unwrap command and that totally
> >> worked!!
> >> >>> >> > Thanks! I'll be sure to include that from now on. I didn't
> realize
> >> >>> that
> >> >>> >> was
> >> >>> >> > required at first because the diffusion command automatically
> >> >>> accounted
> >> >>> >> for
> >> >>> >> > wrapping around in one dimension at a time.
> >> >>> >> >
> >> >>> >> > On Tue, Mar 8, 2016 at 5:34 PM, David A Case <
> >> david.case.rutgers.edu>
> >> >>> >> wrote:
> >> >>> >> >
> >> >>> >> >> On Tue, Mar 08, 2016, Timothy Christopher Schutt wrote:
> >> >>> >> >> >
> >> >>> >> >> > ...one molecule sitting on the box edge or corner happens to
> >> cross
> >> >>> the
> >> >>> >> >> > boundary in two different dimensions during the same frame
> >> change.
> >> >>> In
> >> >>> >> >> > this scenario the wrapping of the second periodic boundary
> is
> >> not
> >> >>> >> >> > accounted for and the MSD jumps up by n * L^2/N (L=
> simulation
> >> box
> >> >>> >> >> > length. n= number of molecules in the mask double wrapping
> that
> >> >>> frame,
> >> >>> >> >> > and N = the number of molecules in the mask).
> >> >>> >> >>
> >> >>> >> >> Are you trying to compute diffusion behavior from a trajectory
> >> that
> >> >>> was
> >> >>> >> >> originally created with iwrap=1? Or that has been subject to
> the
> >> >>> >> "image"
> >> >>> >> >> or
> >> >>> >> >> "autoimage" command in cpptraj? Just trying to pin down
> possible
> >> >>> >> sources
> >> >>> >> >> of
> >> >>> >> >> problems.
> >> >>> >> >>
> >> >>> >> >> ....dac
> >> >>> >> >>
> >> >>> >> >>
> >> >>> >> >> _______________________________________________
> >> >>> >> >> 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
> >> >>> >>
> >> >>> >>
> >> >>> >>
> >> >>> >> --
> >> >>> >> -------------------------
> >> >>> >> Daniel R. Roe, PhD
> >> >>> >> Department of Medicinal Chemistry
> >> >>> >> University of Utah
> >> >>> >> 30 South 2000 East, Room 307
> >> >>> >> Salt Lake City, UT 84112-5820
> >> >>> >> http://home.chpc.utah.edu/~cheatham/
> >> >>> >> (801) 587-9652
> >> >>> >> (801) 585-6208 (Fax)
> >> >>> >>
> >> >>> >> _______________________________________________
> >> >>> >> 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
> >> >>>
> >> >>>
> >> >>>
> >> >>> --
> >> >>> -------------------------
> >> >>> Daniel R. Roe, PhD
> >> >>> Department of Medicinal Chemistry
> >> >>> University of Utah
> >> >>> 30 South 2000 East, Room 307
> >> >>> Salt Lake City, UT 84112-5820
> >> >>> http://home.chpc.utah.edu/~cheatham/
> >> >>> (801) 587-9652
> >> >>> (801) 585-6208 (Fax)
> >> >>>
> >> >>> _______________________________________________
> >> >>> 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
> >> >
> >> >
> >> >
> >> > --
> >> > -------------------------
> >> > Daniel R. Roe, PhD
> >> > Department of Medicinal Chemistry
> >> > University of Utah
> >> > 30 South 2000 East, Room 307
> >> > Salt Lake City, UT 84112-5820
> >> > http://home.chpc.utah.edu/~cheatham/
> >> > (801) 587-9652
> >> > (801) 585-6208 (Fax)
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> 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
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Mar 09 2016 - 13:30:03 PST
