On Wed, Mar 9, 2016 at 2:13 PM, Timothy Christopher Schutt
<tschutt.mymail.mines.edu> wrote:
> 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!
Yeah, the non-orthorhombic correction is something I just implemented
(there has been an orthorhombic one since the days of ptraj). It's
actually faster than having a prior 'unwrap' as well. Glad to hear
it's working for you!
-Dan
>
> 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
>>
> _______________________________________________
> 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)
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Received on Thu Mar 10 2016 - 08:30:08 PST
